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- PDB-1amz: CHICKEN CITRATE SYNTHASE COMPLEX WITH NITROMETHYLDE-COA AND MALATE -

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Basic information

Entry
Database: PDB / ID: 1amz
TitleCHICKEN CITRATE SYNTHASE COMPLEX WITH NITROMETHYLDE-COA AND MALATE
ComponentsCITRATE SYNTHASE
KeywordsOXO-ACID-LYASE / TRICARBOXYLIC ACID CYCLE / ALLOSTERIC ENZYME
Function / homology
Function and homology information


The tricarboxylic acid cycle / citrate (Si)-synthase / citrate synthase activity / : / citrate metabolic process / tricarboxylic acid cycle / carbohydrate metabolic process / mitochondrial matrix / mitochondrion / identical protein binding
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
D-MALATE / NITROMETHYLDETHIA COENZYME A / Citrate synthase, mitochondrial
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR SUBSTITUTION / Resolution: 1.8 Å
AuthorsUsher, K.C. / Remington, S.J.
Citation
Journal: To be Published
Title: Mechanisms of Enzyme-Catalyzed Deprotonation of Acetyl-Coenzyme A
Authors: Schwartz, B. / Vogel, K.W. / Usher, K.C. / Narasimhan, C. / Miziorko, H.M. / Remington, S.J. / Drueckhammer, D.G.
#1: 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.
#2: Journal: Biochemistry / Year: 1990
Title: Proposed Mechanism for the Condensation Reaction of Citrate Synthase: 1.9-A Structure of the Ternary Complex with Oxaloacetate and Carboxymethyl Coenzyme A
Authors: Karpusas, M. / Branchaud, B. / Remington, S.J.
#3: 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.
#4: 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 A Resolution
Authors: Remington, S. / Wiegand, G. / Huber, R.
History
DepositionJun 19, 1997Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Category: pdbx_unobs_or_zero_occ_atoms
Revision 1.4Aug 2, 2023Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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 1.5Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CITRATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1043
Polymers48,1751
Non-polymers9292
Water2,540141
1
A: CITRATE SYNTHASE
hetero molecules

A: CITRATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2076
Polymers96,3502
Non-polymers1,8574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area13460 Å2
ΔGint-49 kcal/mol
Surface area28250 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)104.127, 78.500, 58.420
Angle α, β, γ (deg.)90.00, 78.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CITRATE SYNTHASE


Mass: 48174.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Cellular location: INNER MATRIX / Organ: HEART / Organelle: MITOCHONDRIA / Tissue: MUSCLE / References: UniProt: P23007, EC: 4.1.3.7
#2: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#3: Chemical ChemComp-NMX / NITROMETHYLDETHIA COENZYME A


Mass: 794.493 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H37N8O18P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.4 Å3/Da / Density % sol: 55 %
Crystal growpH: 6
Details: CRYSTALLIZED FROM 1.01M NA MALATE, PH 6.0 2 MM NITROMETHYLDETHIA COENZYME A THE CELL ANGLE BETA IS DEFINED AS THE ACUTE ANGLE FOR CONSISTENCY WITH PREVIOUS PDB ENTRIES OF CITRATE SYNTHASE IN THIS SPACE GROUP

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Mar 12, 1997 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 36528 / % possible obs: 85 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 8.6
Reflection shellResolution: 1.8→1.94 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 2.1 / % possible all: 75

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Processing

Software
NameVersionClassification
TNTrefinement
SDMS(DCREDUCE)data reduction
SDMS(SCALE)data scaling
TNTphasing
RefinementMethod to determine structure: MOLECULAR SUBSTITUTION
Starting model: PDB ENTRY 1CSH

1csh


Resolution: 1.8→25 Å / Isotropic thermal model: TNT BCORREL V1.0 / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rwork0.154 --
all-36675 -
obs-36675 85 %
Solvent computationSolvent model: BABINET SCALING / Bsol: 680 Å2 / ksol: 1.07 e/Å3
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3391 0 60 141 3592
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01435451
X-RAY DIFFRACTIONt_angle_deg2.147912
X-RAY DIFFRACTIONt_dihedral_angle_d16.120470
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.018811
X-RAY DIFFRACTIONt_gen_planes0.0165095
X-RAY DIFFRACTIONt_it4.734761
X-RAY DIFFRACTIONt_nbd0.0161120

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