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- PDB-1qb4: CRYSTAL STRUCTURE OF MN(2+)-BOUND PHOSPHOENOLPYRUVATE CARBOXYLASE -

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Basic information

Entry
Database: PDB / ID: 1qb4
TitleCRYSTAL STRUCTURE OF MN(2+)-BOUND PHOSPHOENOLPYRUVATE CARBOXYLASE
ComponentsPHOSPHOENOLPYRUVATE CARBOXYLASE
KeywordsLYASE / ALPHA BETA BARREL
Function / homology
Function and homology information


phosphoenolpyruvate carboxylase / phosphoenolpyruvate carboxylase activity / carbon fixation / oxaloacetate metabolic process / tricarboxylic acid cycle / gluconeogenesis / protein homotetramerization / magnesium ion binding / identical protein binding / cytosol
Similarity search - Function
Phosphoenolpyruvate carboxylase, Lys active site / Phosphoenolpyruvate carboxylase / Phosphoenolpyruvate carboxylase, bacterial/plant-type / Phosphoenolpyruvate carboxylase, His active site / Phosphoenolpyruvate carboxylase / Phosphoenolpyruvate carboxylase active site 2. / Phosphoenolpyruvate carboxylase active site 1. / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
ASPARTIC ACID / : / Phosphoenolpyruvate carboxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsMatsumura, H. / Terada, M. / Shirakata, S. / Inoue, T. / Yoshinaga, T. / Izui, K. / Kai, Y.
Citation
Journal: FEBS Lett. / Year: 1999
Title: Plausible phosphoenolpyruvate binding site revealed by 2.6 A structure of Mn2+-bound phosphoenolpyruvate carboxylase from Escherichia coli
Authors: Matsumura, H. / Terada, M. / Shirakata, S. / Inoue, T. / Yoshinaga, T. / Izui, K. / Kai, Y.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Three-dimensional Structure of Phosphoenolpyruvate Carboxylase: A proposed mechanism for allosteric inhibition
Authors: Kai, Y. / Matsumura, H. / Inoue, T. / Terada, K. / Nagara, Y. / Yoshinaga, T. / Kihara, A. / Tsumura, K. / Izui, K.
History
DepositionApr 30, 1999Deposition site: RCSB / Processing site: NDB
Revision 1.0May 1, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 23, 2018Group: Data collection / Derived calculations / Category: pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[3][3] ..._pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3]
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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

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Assembly

Deposited unit
A: PHOSPHOENOLPYRUVATE CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,3643
Polymers99,1751
Non-polymers1882
Water1,45981
1
A: PHOSPHOENOLPYRUVATE CARBOXYLASE
hetero molecules

A: PHOSPHOENOLPYRUVATE CARBOXYLASE
hetero molecules

A: PHOSPHOENOLPYRUVATE CARBOXYLASE
hetero molecules

A: PHOSPHOENOLPYRUVATE CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)397,45412
Polymers396,7024
Non-polymers7528
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)117.750, 248.410, 83.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsThe biological assembly is a tetramer.

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Components

#1: Protein PHOSPHOENOLPYRUVATE CARBOXYLASE


Mass: 99175.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: K12 / Production host: Escherichia coli (E. coli)
References: UniProt: P00864, phosphoenolpyruvate carboxylase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 300, MANGANESE SULPHATE, SUCROSE., pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
250 mMTris-HCl1droppH7.4
36 mMNa-L-Asp1drop
445 mM1dropCaCl2
50.6 mMdithiothreitol1drop
60.6 Msucrose1drop
720 mM1dropMnSO4
810 %(w/v)PEG3001drop
92.5 mMNa-L-Asp1reservoir
1090 mM1reservoirCaCl2
110.25 mMdithiothreitol1reservoir
1215 %(w/v)PEG3001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Dec 6, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 34597 / Num. obs: 34589 / % possible obs: 90.9 % / Observed criterion σ(F): 0.5 / Observed criterion σ(I): 0.5 / Redundancy: 4.56 % / Biso Wilson estimate: 42.832 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 10.6
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.249 / Num. unique all: 3145 / % possible all: 83.6
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 34597 / % possible obs: 90.7 % / Num. measured all: 157727 / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
Rmerge(I) obs: 0.249

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.6→20 Å / σ(F): 0.5 / σ(I): 0.5
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1091 -RANDOM
Rwork0.223 ---
all0.221 34597 --
obs0.221 33439 87.9 %-
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6835 0 10 81 6926
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_deg1.8
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.221 / Rfactor Rfree: 0.261 / Rfactor Rwork: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS

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