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- PDB-1nxe: A Novel NADH Allosteric Regulator Site is Found on the Surface of... -

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Basic information

Entry
Database: PDB / ID: 1nxe
TitleA Novel NADH Allosteric Regulator Site is Found on the Surface of the Hexameric Type II Phe383Ala Variant of Citrate Synthase
ComponentsCitrate synthase
KeywordsTRANSFERASE / citrate synthase / NADH / allosteric
Function / homology
Function and homology information


citrate synthase (unknown stereospecificity) / : / 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: 2.3 Å
AuthorsMaurus, R. / Nguyen, N.T. / Stokell, D.J. / Ayed, A. / Hultin, P.G. / Duckworth, H.W. / Brayer, G.D.
CitationJournal: Biochemistry / Year: 2003
Title: Insights into the evolution of allosteric properties. The NADH binding site of hexameric type II citrate synthases.
Authors: Maurus, R. / Nguyen, N.T. / Stokell, D.J. / Ayed, A. / Hultin, P.G. / Duckworth, H.W. / Brayer, G.D.
History
DepositionFeb 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2003Provider: 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)96,6748
Polymers96,0982
Non-polymers5766
Water13,079726
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)290,02324
Polymers288,2936
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
Unit cell
Length a, b, c (Å)165.243, 165.243, 157.557
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: 48048.902 Da / Num. of mol.: 2 / Mutation: F383A
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


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


Mass: 18.015 Da / Num. of mol.: 726 / 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: 4.31 Å3/Da / Density % sol: 71.44 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12-2.2 Mammonium sulfate1reservoir
22 %(v/v)PEG4001reservoir
30.1 Msodium HEPES1reservoirpH7.5
420 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorDate: Feb 7, 2002
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 54292 / Observed criterion σ(I): 0
Reflection
*PLUS
Lowest resolution: 50 Å / Redundancy: 3.8 % / Num. measured all: 485765 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.34 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.154 / Mean I/σ(I) obs: 8.6

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Processing

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

1k3p
PDB Unreleased entry


Resolution: 2.3→10 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rwork0.17 --
obs0.17 53934 77 %
all-53934 -
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6719 0 30 726 7475
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor obs: 0.17 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.007
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.6

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