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- PDB-3lye: Crystal structure of oxaloacetate acetylhydrolase -

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Basic information

Entry
Database: PDB / ID: 3lye
TitleCrystal structure of oxaloacetate acetylhydrolase
ComponentsOxaloacetate acetyl hydrolase
KeywordsHYDROLASE / (alpha/beta)8 barrel
Function / homologyPhosphoenolpyruvate-binding domains / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Function and homology information
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsHerzberg, O. / Chen, C.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structure of oxalacetate acetylhydrolase, a virulence factor of the chestnut blight fungus.
Authors: Chen, C. / Sun, Q. / Narayanan, B. / Nuss, D.L. / Herzberg, O.
History
DepositionFeb 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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: Oxaloacetate acetyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2244
Polymers33,1041
Non-polymers1203
Water7,386410
1
A: Oxaloacetate acetyl hydrolase
hetero molecules

A: Oxaloacetate acetyl hydrolase
hetero molecules

A: Oxaloacetate acetyl hydrolase
hetero molecules

A: Oxaloacetate acetyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,89616
Polymers132,4154
Non-polymers48112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_554y,x,-z-11
crystal symmetry operation8_554-y,-x,-z-11
Buried area20030 Å2
ΔGint-241 kcal/mol
Surface area38420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.736, 82.736, 73.846
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-743-

HOH

21A-772-

HOH

31A-833-

HOH

41A-854-

HOH

51A-861-

HOH

61A-977-

HOH

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Components

#1: Protein Oxaloacetate acetyl hydrolase


Mass: 33103.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The fist four residues in the sequence are from the plasmid, not the source gene.
Source: (gene. exp.) Cryphonectria parasitica (chestnut blight fungus)
Gene: OAH / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: oxaloacetase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 1.91 Å3/Da / Density % sol: 35.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG 400, 0.1 M HEPES pH7.5, 0.2M CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→45.9 Å / Num. all: 63521 / Num. obs: 58937 / % possible obs: 92.8 % / Redundancy: 13.7 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 36.2
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 2.7 / % possible all: 50.7

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.3refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FA3

3fa3


Resolution: 1.3→45.9 Å / SU ML: 0.14 / Isotropic thermal model: Isotropic / Phase error: 14.14 / Details: HYDROGENS ARE REFINED AS RIDING MODEL
RfactorNum. reflection% reflection
Rfree0.166 3014 -
Rwork0.131 --
all-63521 -
obs-58937 92.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.59 Å2 / ksol: 0.423 e/Å3
Displacement parametersBiso mean: 17.9 Å2
Refinement stepCycle: LAST / Resolution: 1.3→45.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2159 0 3 410 2572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014358
X-RAY DIFFRACTIONf_angle_d1.37887
X-RAY DIFFRACTIONf_dihedral_angle_d16.71102
X-RAY DIFFRACTIONf_chiral_restr0.12341
X-RAY DIFFRACTIONf_plane_restr0.006673
LS refinement shellResolution: 1.3→1.35 Å
RfactorNum. reflection% reflection
Rfree0.301 175 -
Rwork0.249 0 -
obs--57 %

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