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- PDB-3m0j: Structure of oxaloacetate acetylhydrolase in complex with the inh... -

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Basic information

Entry
Database: PDB / ID: 3m0j
TitleStructure of oxaloacetate acetylhydrolase in complex with the inhibitor 3,3-difluorooxalacetate
ComponentsOxaloacetate acetyl hydrolase
KeywordsHYDROLASE / (alpha/beta)8 barrel
Function / homologyPhosphoenolpyruvate-binding domains / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / : / 2,2-difluoro-3,3-dihydroxybutanedioic acid
Function and homology information
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 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
DepositionMar 3, 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.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.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)33,3854
Polymers33,1041
Non-polymers2813
Water5,999333
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)133,54016
Polymers132,4154
Non-polymers1,12412
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 area21370 Å2
ΔGint-220 kcal/mol
Surface area36590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.144, 82.144, 72.660
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-926-

HOH

21A-927-

HOH

31A-928-

HOH

41A-929-

HOH

51A-930-

HOH

61A-931-

HOH

71A-932-

HOH

81A-933-

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
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-OAF / 2,2-difluoro-3,3-dihydroxybutanedioic acid


Mass: 186.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4F2O6
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 1.85 Å3/Da / Density % sol: 33.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: LIGAND-FREE PROTEIN CRYSTAL GROWN IN SOLUTION CONTAINING 30% PEG 400, 0.1 M HEPES pH7.5, 0.2 M CaCl2, THEN SOAKED IN MOTHER LIQUOR CONTAINING 0.2M MNCL2 AND 20 mM INHIBITOR FOR 15 min, VAPOR ...Details: LIGAND-FREE PROTEIN CRYSTAL GROWN IN SOLUTION CONTAINING 30% PEG 400, 0.1 M HEPES pH7.5, 0.2 M CaCl2, THEN SOAKED IN MOTHER LIQUOR CONTAINING 0.2M MNCL2 AND 20 mM INHIBITOR FOR 15 min, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationMonochromator: Xenocs optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→20 Å / Num. all: 36658 / Num. obs: 36608 / % possible obs: 99.9 % / Redundancy: 10.6 % / Biso Wilson estimate: 12.5 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 21.1
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 3.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LYE

3lye


Resolution: 1.55→19.92 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.18 / Isotropic thermal model: Isotropic / σ(F): 1.48 / Phase error: 19.7 / Stereochemistry target values: ML
Details: ANISOTROPIC B VALUES DERIVED FROM FROM TLS REFINEMENT, HYDROGENS ARE INCLUDED AS RIDING MODEL
RfactorNum. reflection% reflection
Rfree0.201 1875 5.12 %
Rwork0.175 --
obs0.176 36608 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 81.42 Å2 / ksol: 0.44 e/Å3
Displacement parametersBiso mean: 22.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.145 Å20 Å2-0 Å2
2--0.145 Å20 Å2
3----0.289 Å2
Refinement stepCycle: LAST / Resolution: 1.55→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2250 0 14 333 2597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064565
X-RAY DIFFRACTIONf_angle_d0.9398253
X-RAY DIFFRACTIONf_dihedral_angle_d16.3381174
X-RAY DIFFRACTIONf_chiral_restr0.073353
X-RAY DIFFRACTIONf_plane_restr0.004705
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.59190.35951490.33092614X-RAY DIFFRACTION100
1.5919-1.63870.34731480.2992603X-RAY DIFFRACTION100
1.6387-1.69160.29091420.28682630X-RAY DIFFRACTION100
1.6916-1.7520.31361300.25642644X-RAY DIFFRACTION100
1.752-1.82210.29411470.22952634X-RAY DIFFRACTION100
1.8221-1.9050.22991480.18792625X-RAY DIFFRACTION100
1.905-2.00530.21061310.15732667X-RAY DIFFRACTION100
2.0053-2.13080.16151350.1432656X-RAY DIFFRACTION100
2.1308-2.29510.16751460.13172672X-RAY DIFFRACTION100
2.2951-2.52570.17451450.13722677X-RAY DIFFRACTION100
2.5257-2.89020.1421480.13242699X-RAY DIFFRACTION100
2.8902-3.63770.15871380.1312750X-RAY DIFFRACTION100
3.6377-19.92450.16881680.16692862X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.33910.02230.11310.598-0.26740.4519-0.00960.0112-0.00160.0899-0.0195-0.0798-0.02490.0638-0.00010.06770.0009-0.0170.05880.01070.082518.33712.3215-26.0254
20.01610.01340.09090.1442-0.08430.1139-0.02280.01780.03080.07720.0021-0.0662-0.04180.0084-0.00510.08510.0041-0.02190.060.00270.073419.11040.7923-25.526
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESIDUE 68-364
2X-RAY DIFFRACTION2NOT (CHAIN A AND RESIDUE 68-364)

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