[English] 日本語
Yorodumi
- PDB-1gpm: ESCHERICHIA COLI GMP SYNTHETASE COMPLEXED WITH AMP AND PYROPHOSPHATE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gpm
TitleESCHERICHIA COLI GMP SYNTHETASE COMPLEXED WITH AMP AND PYROPHOSPHATE
ComponentsGMP SYNTHETASEGMP synthase
KeywordsTRANSFERASE (GLUTAMINE AMIDOTRANSFERASE) / CLASS I GLUTAMINE AMIDOTRANSFERASE / N-TYPE ATP PYROPHOSPHATASE
Function / homology
Function and homology information


GMP synthase activity / GMP synthase (glutamine-hydrolyzing) activity / GMP synthase (glutamine-hydrolysing) / pyrophosphatase activity / GMP biosynthetic process / glutamine metabolic process / ATP binding / identical protein binding / cytosol
Similarity search - Function
GMP synthase / GMP synthase, C-terminal / GMP synthetase ATP pyrophosphatase domain / GMP synthase C terminal domain / GMP synthetase ATP pyrophosphatase (GMPS ATP-PPase) domain profile. / GMP synthase, glutamine amidotransferase / GMP Synthetase; Chain A, domain 3 - #10 / NAD/GMP synthase / NAD synthase / Glutamine amidotransferase class-I ...GMP synthase / GMP synthase, C-terminal / GMP synthetase ATP pyrophosphatase domain / GMP synthase C terminal domain / GMP synthetase ATP pyrophosphatase (GMPS ATP-PPase) domain profile. / GMP synthase, glutamine amidotransferase / GMP Synthetase; Chain A, domain 3 - #10 / NAD/GMP synthase / NAD synthase / Glutamine amidotransferase class-I / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / GMP Synthetase; Chain A, domain 3 / Class I glutamine amidotransferase-like / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / CITRIC ACID / PHOSPHATE ION / PYROPHOSPHATE 2- / GMP synthase [glutamine-hydrolyzing]
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsTesmer, J.J.G.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: The crystal structure of GMP synthetase reveals a novel catalytic triad and is a structural paradigm for two enzyme families.
Authors: Tesmer, J.J. / Klem, T.J. / Deras, M.L. / Davisson, V.J. / Smith, J.L.
#1: Journal: Proteins / Year: 1994
Title: Preliminary X-Ray Analysis of Escherichia Coli Gmp Synthetase: Determination of Anomalous Scattering Factors for a Cysteinyl Mercury Derivative
Authors: Tesmer, J.J.G. / Stemmler, T.L. / Penner-Hahn, J.E. / Davisson, V.J. / Smith, J.L.
History
DepositionApr 4, 1995Processing site: BNL
Revision 1.0Jan 29, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX HELIX DETERMINATION METHOD: RESIDUES FORMING SECONDARY STRUCTURE HAVE BACKBONE H-BONDS < 3.4 ...HELIX HELIX DETERMINATION METHOD: RESIDUES FORMING SECONDARY STRUCTURE HAVE BACKBONE H-BONDS < 3.4 ANGSTROMS HELIX_ID: 5A,LAST 2 RESIDUES FORM PI H-BONDS. HELIX_ID: 8A,LAST 2 RESIDUES FORM PI H-BONDS. HELIX_ID: 5B,LAST 2 RESIDUES FORM PI H-BONDS. HELIX_ID: 8B,LAST 2 RESIDUES FORM PI H-BONDS. HELIX_ID: 5C,LAST 2 RESIDUES FORM PI H-BONDS. HELIX_ID: 8C,LAST 2 RESIDUES FORM PI H-BONDS. HELIX_ID: 5D,LAST 2 RESIDUES FORM PI H-BONDS. HELIX_ID: 8D,LAST 2 RESIDUES FORM PI H-BONDS.
Remark 700SHEET S1A, S1B, S1C, S1D: DETERMINATION METHOD: RESIDUES FORMING SECONDARY STRUCTURE HAVE BACKBONE ...SHEET S1A, S1B, S1C, S1D: DETERMINATION METHOD: RESIDUES FORMING SECONDARY STRUCTURE HAVE BACKBONE H-BONDS < 3.4 ANGSTROMS; S1A AND S2A, S1B AND S2B, S1C AND S2C, S1D AND S2D ARE CONTINUOUS, BUT THE OVERALL FOLD OF THE DOMAIN SUGGESTS THAT THEY ARE BETTER DESCRIBED AS DISTINCT SHEETS. THE FIRST STRAND IN S2A, S2B, S2C, S2D WOULD BE THE NEXT STRAND IN S1A S1B, S1C, S1D, RESPECTIVELY. S3A, S3B, S3C, S3D: BETA RIBBON. THE DIMERIZATION DOMAIN FOR CHAINS A AND C CONTAINS A SHEET WITH TWO BIFURCATED STRANDS, AS DOES THE DIMERIZATION DOMAIN FOR CHAINS B AND D. THESE SHEETS ARE PRESENTED AS SHEETS SAC AND TAC FOR CHAINS A AND C AND SHEETS SBD AND TBD FOR CHAINS B AND D. SHEETS SAC AND TAC DIFFER IN CHAINS 3 AND 4 AS DO SHEETS SBD AND TBD. SBD: DIMERIZATION DOMAIN. ATOM_NAME: () () CYS A 86 () CYS 86 HAS A STRAINED BACKBONE CONFORMATION (PHI=55, PSI= -110) TYPICAL OF "NUCLEOPHILE ELBOWS" FOUND IN THE A/B HYDROLASES. THE RESIDUE IS BOTH A MEMBER OF SHEET S1A AND HELIX 4A. ATOM_NAME: () () CYS B 86 () CYS 86 HAS A STRAINED BACKBONE CONFORMATION (PHI=55, PSI= -110) TYPICAL OF "NUCLEOPHILE ELBOWS" FOUND IN THE A/B HYDROLASES. THE RESIDUE IS BOTH A MEMBER OF SHEET S1B AND HELIX 4B. ATOM_NAME: () () CYS C 86 () CYS 86 HAS A STRAINED BACKBONE CONFORMATION (PHI=55, PSI= -110) TYPICAL OF "NUCLEOPHILE ELBOWS" FOUND IN THE A/B HYDROLASES. THE RESIDUE IS BOTH A MEMBER OF SHEET S1C AND HELIX 4C. ATOM_NAME: () () CYS D 86 () CYS 86 HAS A STRAINED BACKBONE CONFORMATION (PHI=55, PSI= -110) TYPICAL OF "NUCLEOPHILE ELBOWS" FOUND IN THE A/B HYDROLASES. THE RESIDUE IS BOTH A MEMBER OF SHEET S1D AND HELIX 4D.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GMP SYNTHETASE
B: GMP SYNTHETASE
C: GMP SYNTHETASE
D: GMP SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,31423
Polymers235,0004
Non-polymers3,31419
Water14,232790
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17290 Å2
ΔGint-116 kcal/mol
Surface area80690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.000, 102.000, 78.800
Angle α, β, γ (deg.)90.00, 96.70, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO A 518 / 2: CIS PROLINE - PRO A 519 / 3: CIS PROLINE - PRO B 518 / 4: CIS PROLINE - PRO B 519 / 5: CIS PROLINE - PRO C 518 / 6: CIS PROLINE - PRO C 519 / 7: CIS PROLINE - PRO D 518 / 8: CIS PROLINE - PRO D 519

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
GMP SYNTHETASE / GMP synthase / XMP AMINASE


Mass: 58750.043 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Description: TAC PROMOTER / Gene: GUAA / Plasmid: PGUAA-TAC / Gene (production host): GUAA / Production host: Escherichia coli (E. coli)
References: UniProt: P04079, GMP synthase (glutamine-hydrolysing)

-
Non-polymers , 6 types, 809 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2O7P2
#4: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Chemical
ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 790 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsN-TERMINAL SEQUENCING INDICATES THAT 50% OF THE N-TERMINAL METHIONINES ARE CLEAVED IN THE PURIFIED PROTEIN.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.6553.56
2
Crystal growpH: 5 / Details: pH 5.0
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18.5 mg/mlGMPS1drop
234 mMsodium citrate1drop
33 mM1dropMgCl2
40.75 mMATP1drop
50.75 mM5'-monophosphate1drop
65 mMDTE1drop
71 mMEDTA1drop
82.0-2.67 %PEG80001drop
950 mMsodium citrate1reservoir
1010 %PEG80001reservoir

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12771
22772
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)Wavelength
SYNCHROTRONPhoton Factory BL-6A10.9100, 0.9804
ROTATING ANODERIGAKU RU20021.5418
Detector
TypeIDDateDetector
WEISSENBERG1Mar 15, 1993
XUONG-HAMLIN MULTIWIRE21992AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911
20.98041
31.54181
ReflectionResolution: 2.2→50 Å / Num. obs: 105224 / % possible obs: 84.5 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.053
Reflection
*PLUS
% possible obs: 841.4 % / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
% possible obs: 48.4 % / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 8.7

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSMODIFIED FOR USE WITH SDMSdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.2→6 Å /
RfactorNum. reflection
Rwork0.174 -
obs0.174 98760
Displacement parametersBiso mean: 35.3 Å2
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15804 0 203 790 16797
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more