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- PDB-4g6b: Three dimensional structure analysis of the type II citrate synth... -

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Basic information

Entry
Database: PDB / ID: 4g6b
TitleThree dimensional structure analysis of the type II citrate synthase from e.coli
ComponentsCitrate synthase
KeywordsTRANSFERASE / CITRATE SYNTHASE
Function / homology
Function and homology information


citrate synthase (unknown stereospecificity) / citrate (Si)-synthase activity / NADH binding / protein hexamerization / tricarboxylic acid cycle / identical protein binding / cytosol
Similarity search - Function
Rubrerythrin, domain 2 - #60 / Citrate synthase, type I / Citrate synthase, bacterial-type / Citrate Synthase; domain 1 / Citrate Synthase, domain 1 / Cytochrome p450-Terp; domain 2 / Cytochrome P450-Terp, domain 2 / Citrate synthase active site / Citrate synthase signature. / Citrate synthase-like, large alpha subdomain ...Rubrerythrin, domain 2 - #60 / Citrate synthase, type I / Citrate synthase, bacterial-type / Citrate Synthase; domain 1 / Citrate Synthase, domain 1 / Cytochrome p450-Terp; domain 2 / Cytochrome P450-Terp, domain 2 / Citrate synthase active site / Citrate synthase signature. / Citrate synthase-like, large alpha subdomain / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / Rubrerythrin, domain 2 / Single Sheet / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNguyen, N.T. / Maurus, R. / Stokell, D.J. / Ayed, A. / Duckworth, H.W. / Brayer, G.D.
CitationJournal: Biochemistry / Year: 2001
Title: Comparative Analysis of Folding and Substrate Binding Sites between Regulated Hexameric Type II Citrate Synthases and Unregulated Dimeric Type I Enzymes.
Authors: Nguyen, N.T. / Maurus, R. / Stokell, D.J. / Ayed, A. / Duckworth, H.W. / Brayer, G.D.
History
DepositionJul 18, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionNov 20, 2013ID: 1K3P
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Citrate synthase
B: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,4708
Polymers95,8932
Non-polymers5766
Water14,304794
1
A: Citrate synthase
B: Citrate synthase
hetero molecules

A: Citrate synthase
B: Citrate synthase
hetero molecules

A: Citrate synthase
B: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,41024
Polymers287,6806
Non-polymers1,72918
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area48270 Å2
ΔGint-514 kcal/mol
Surface area95600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.375, 165.375, 155.321
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Citrate synthase /


Mass: 47946.742 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0ABH7, citrate (Si)-synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 794 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsASPARTATE AT POSITION 10 IS A POST-TRANSLATIONAL MODIFICATION OF ASN THAT IS CONSISTENTLY OBSERVED ...ASPARTATE AT POSITION 10 IS A POST-TRANSLATIONAL MODIFICATION OF ASN THAT IS CONSISTENTLY OBSERVED IN MASS SPECTROMETRY AND EDMAN DEGRADATION MEASUREMENTS.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.26 Å3/Da / Density % sol: 71.1 %
Crystal growDetails: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 22, 1999 / Details: MIRRORS
RadiationMonochromator: OSMIC CONFOCAL MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→10 Å / Num. obs: 79578 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.93 / Net I/σ(I): 13.3
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.132 / Mean I/σ(I) obs: 6.7 / % possible all: 99.4

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AJ8

1aj8


Resolution: 2.2→10 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.226 3947 -RANDOM
Rwork0.178 ---
obs0.178 78948 100 %-
Displacement parametersBiso mean: 42.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å / Luzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6724 0 30 794 7548
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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