[English] 日本語
Yorodumi
- PDB-4dwd: Crystal structure of mandelate racemase/muconate lactonizing prot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dwd
TitleCrystal structure of mandelate racemase/muconate lactonizing protein from Paracoccus denitrificans PD1222 complexed with magnesium
ComponentsMandelate racemase/muconate lactonizing enzyme, C-terminal domain protein
KeywordsMETAL BINDING PROTEIN / STRUCTURAL GENOMICS / EFI / Enzyme Function Initiative
Function / homology
Function and homology information


hydro-lyase activity / metal ion binding
Similarity search - Function
: / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal ...: / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Mandelate racemase/muconate lactonizing enzyme, C-terminal domain protein
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsMalashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of mandelate racemase/muconate lactonizing protein from Paracoccus denitrificans PD1222 complexed with magnesium
Authors: Malashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionFeb 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Structure summary
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mandelate racemase/muconate lactonizing enzyme, C-terminal domain protein
B: Mandelate racemase/muconate lactonizing enzyme, C-terminal domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,00010
Polymers85,7502
Non-polymers2508
Water14,880826
1
A: Mandelate racemase/muconate lactonizing enzyme, C-terminal domain protein
B: Mandelate racemase/muconate lactonizing enzyme, C-terminal domain protein
hetero molecules

A: Mandelate racemase/muconate lactonizing enzyme, C-terminal domain protein
B: Mandelate racemase/muconate lactonizing enzyme, C-terminal domain protein
hetero molecules

A: Mandelate racemase/muconate lactonizing enzyme, C-terminal domain protein
B: Mandelate racemase/muconate lactonizing enzyme, C-terminal domain protein
hetero molecules

A: Mandelate racemase/muconate lactonizing enzyme, C-terminal domain protein
B: Mandelate racemase/muconate lactonizing enzyme, C-terminal domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)343,99940
Polymers342,9988
Non-polymers1,00132
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z1
Buried area36370 Å2
ΔGint-305 kcal/mol
Surface area85060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.598, 136.598, 80.603
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-501-

MG

21B-501-

MG

-
Components

#1: Protein Mandelate racemase/muconate lactonizing enzyme, C-terminal domain protein


Mass: 42874.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: PD1222 / Gene: Pden_0244 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: A1AYL4
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 826 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 28% PEG 400, 0.1 M NA-HEPES, 0.2 M CA CHLORIDE, soaked for 5 min in 30% PEG400, 0.1M HEPES, pH 7.5, 0.2M MgCl2, 0.1M tartrate, 20% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2010
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. obs: 120795 / % possible obs: 95.5 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.064 / Χ2: 0.917 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.48-1.5110.80.71648880.71178.4
1.51-1.53110.62255230.714188.2
1.53-1.5610.90.55555400.719188.8
1.56-1.5910.80.44656090.748189.7
1.59-1.6310.80.40556520.75190.4
1.63-1.6710.60.34657890.767192.3
1.67-1.7110.50.31359100.775194.1
1.71-1.7510.30.26160000.785196
1.75-1.8110.40.22461260.804197.5
1.81-1.8610.50.17861610.834198.1
1.86-1.9310.50.15761780.953198.4
1.93-2.0110.80.11862690.892199.2
2.01-2.111.20.09562260.883199.3
2.1-2.2111.70.08462850.952199.4
2.21-2.3511.40.08363231.261199.6
2.35-2.5312.60.06463261.119199.7
2.53-2.7912.90.0663851.314199.9
2.79-3.1913.50.04463901.1021100
3.19-4.02120.03264691.046199.7
4.02-5014.20.02667460.831199.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 34.75 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å43.2 Å
Translation2.5 Å43.2 Å

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N4E

3n4e


Resolution: 1.5→19.94 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.1656 / WRfactor Rwork: 0.1386 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.913 / SU B: 1.993 / SU ML: 0.035 / SU R Cruickshank DPI: 0.0774 / SU Rfree: 0.0646 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1724 5889 5 %RANDOM
Rwork0.1417 ---
obs0.1433 116924 96.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.74 Å2 / Biso mean: 15.8271 Å2 / Biso min: 6.29 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5569 0 8 826 6403
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195818
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.9747921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5585775
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83823.123253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.28615883
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.891554
X-RAY DIFFRACTIONr_chiral_restr0.0820.2892
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214454
X-RAY DIFFRACTIONr_rigid_bond_restr2.69635818
X-RAY DIFFRACTIONr_sphericity_free14.1915175
X-RAY DIFFRACTIONr_sphericity_bonded5.66256351
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.199 356 -
Rwork0.156 7086 -
all-7442 -
obs--87.71 %
Refinement TLS params.

T11: 0.0085 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.07150.04240.04580.14050.04650.0844-0.00990.01660.0106-0.01060.0059-0.0025-0.02250.01090.004-0.0026-0.00090.0040.00280.00233.5937-36.43440.5368
20.1211-0.0580.0870.1056-0.01560.1206-0.0087-0.02610.01050.00230.00210.0042-0.022-0.02760.00670.00530.00070.0083-0.00280.0024-18.2398-41.551226.7596
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 374
2X-RAY DIFFRACTION1A500 - 503
3X-RAY DIFFRACTION2B2 - 378
4X-RAY DIFFRACTION2B501 - 504

+
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