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- PDB-1owb: Three Dimensional Structure Analysis Of The Variant R109L NADH Co... -

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Basic information

Entry
Database: PDB / ID: 1owb
TitleThree Dimensional Structure Analysis Of The Variant R109L NADH Complex of Type II Citrate Synthase From E. Coli
ComponentsCitrate synthase
KeywordsTRANSFERASE / Allostery / NADH / Type II Citrate Synthase / E. Coli / R109L
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Citrate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsStokell, D.J. / Donald, L.J. / Maurus, R. / Nguyen, N.T. / Sadler, G. / Choudhary, K. / Hultin, P.G. / Brayer, G.D. / Duckworth, H.W.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Probing the roles of key residues in the unique regulatory NADH binding site of type II citrate synthase of Escherichia coli.
Authors: Stokell, D.J. / Donald, L.J. / Maurus, R. / Nguyen, N.T. / Sadler, G. / Choudhary, K. / Hultin, P.G. / Brayer, G.D. / Duckworth, H.W.
History
DepositionMar 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)98,06510
Polymers96,1622
Non-polymers1,9038
Water8,845491
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)294,19530
Polymers288,4866
Non-polymers5,71024
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
Unit cell
Length a, b, c (Å)165.001, 165.001, 157.774
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: 48080.957 Da / Num. of mol.: 2 / Mutation: R109L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: GLTA OR GLUT OR ICDB OR B0720 / Production host: Escherichia coli (E. coli) / 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: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 491 / Source method: isolated from a natural source / Formula: H2O

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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: 4.3 Å3/Da / Density % sol: 71.37 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 10, 2000 / Details: osmic mirrors
RadiationMonochromator: Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 76417 / % possible obs: 92 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.083

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K3P

1k3p
PDB Unreleased entry


Resolution: 2.2→10 Å / σ(F): 0 / σ(I): 0 /
RfactorNum. reflection
Rfree0.219 -
Rwork0.162 -
obs-74765
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6726 0 118 491 7335
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.6

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