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- PDB-1csh: A very short hydrogen bond provides only moderate stabilization o... -

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Basic information

Entry
Database: PDB / ID: 1csh
TitleA very short hydrogen bond provides only moderate stabilization of an enzyme: inhibitor complex of citrate synthase
ComponentsCITRATE SYNTHASE
KeywordsLYASE(OXO-ACID)
Function / homology
Function and homology information


citrate (Si)-synthase / The tricarboxylic acid cycle / citrate (Si)-synthase activity / citrate synthase activity / citrate metabolic process / tricarboxylic acid cycle / carbohydrate metabolic process / mitochondrial matrix / mitochondrion
Similarity search - Function
Citrate synthase, eukaryotic-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, eukaryotic-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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
AMIDOCARBOXYMETHYLDETHIA COENZYME *A / OXALOACETATE ION / Citrate synthase, mitochondrial
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 1.65 Å
AuthorsUsher, K.C. / Remington, S.J.
Citation
Journal: Biochemistry / Year: 1994
Title: A very short hydrogen bond provides only moderate stabilization of an enzyme-inhibitor complex of citrate synthase.
Authors: Usher, K.C. / Remington, S.J. / Martin, D.P. / Drueckhammer, D.G.
#1: Journal: Biochemistry / Year: 1990
Title: Proposed Mechanism for the Condensation Reaction of Citrate Synthase. 1.9-Angstroms Structure of the Ternary Complex with Oxaloacetate and Carboxymethyl Coenzyme A
Authors: Karpusas, M. / Branchaud, B. / Remington, S.J.
#2: Journal: J.Mol.Biol. / Year: 1984
Title: Crystal Structure Analysis and Molecular Model of a Complex of Citrate Synthase with Oxaloacetate and S-Acetonyl-Coenzyme A
Authors: Wiegand, G. / Remington, S. / Deisenhofer, J. / Huber, R.
#3: Journal: J.Mol.Biol. / Year: 1982
Title: Crystallographic Refinement and Atomic Models of Two Different Forms of Citrate Synthase at 2.7 And 1.7 Angstroms Resolution
Authors: Remington, S. / Wiegand, G. / Huber, R.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1981
Title: Primary Structure of Porcine Heart Citrate Synthase
Authors: Bloxham, D.P. / Parmelee, D.C. / Kumar, S. / Wade, R.D. / Ericsson, L.H. / Neurath, H. / Walsh, K.A. / Titani, K.
#5: Journal: Eur.J.Biochem. / Year: 1979
Title: Crystal Structure Analysis of the Tetragonal Crystal Form and Preliminary Molecular Model of Pig-Heart Citrate Synthase
Authors: Wiegand, G. / Kukla, D. / Scholze, H. / Jones, T.A. / Huber, R.
History
DepositionMar 7, 1994Processing site: BNL
Revision 1.0Apr 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Feb 7, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CITRATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0993
Polymers48,1751
Non-polymers9242
Water2,612145
1
A: CITRATE SYNTHASE
hetero molecules

A: CITRATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1976
Polymers96,3502
Non-polymers1,8474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area13550 Å2
ΔGint-39.1 kcal/mol
Surface area28000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.400, 78.500, 58.500
Angle α, β, γ (deg.)90.00, 78.90, 90.00
Int Tables number5
Space group name H-MC121
DetailsTHE MOLECULE IS A DIMER, WITH ONE MONOMER OF MOLECULAR WEIGHT 50000 IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT. THE SYMMETRY-RELATED MONOMER CAN BE GENERATED BY THE FOLLOWING CRYSTALLOGRAPHIC TWO-FOLD OPERATION, XS = - XO YS = YO ZS = - ZO WHERE (XO,YO,ZO) ARE THE COORDINATES IN THIS ENTRY AND (XS,YS,ZS) ARE THE SYMMETRY-RELATED SET.

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Components

#1: Protein CITRATE SYNTHASE /


Mass: 48174.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / References: UniProt: P23007, EC: 4.1.3.7
#2: Chemical ChemComp-OAA / OXALOACETATE ION / Oxaloacetic acid


Mass: 131.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3O5
#3: Chemical ChemComp-AMX / AMIDOCARBOXYMETHYLDETHIA COENZYME *A


Mass: 792.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H39N8O17P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.2 mMenzyme1drop
20.5 Mcitrate1drop
35 mMoxaloacetate1drop
40.5 mMinhibitor1drop
50.9-1.1 Msodium citrate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.65 Å / Num. obs: 43148 / Num. measured all: 73408 / Rmerge(I) obs: 0.039

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 1.65→25 Å / σ(F): 0 /
RfactorNum. reflection
obs0.164 43148
Refinement stepCycle: LAST / Resolution: 1.65→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3391 0 60 145 3596
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONt_angle_deg2.7
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.164
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg

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