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- PDB-4c5z: Crystal structure of A. niger ochratoxinase -

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Basic information

Entry
Database: PDB / ID: 4c5z
TitleCrystal structure of A. niger ochratoxinase
ComponentsOCHRATOXINASE
KeywordsHYDROLASE / METAL-DEPENDENT AMIDOHYDROLASE / OCHRATOXIN A HYDROLYSIS / AMIDOHYDROLASE SUPERFAMILY
Function / homology
Function and homology information


ochratoxin A catabolic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / carboxypeptidase activity / metallopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel ...Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Ochratoxinase / Amidohydro-rel domain-containing protein
Similarity search - Component
Biological speciesASPERGILLUS NIGER (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDobritzsch, D. / Wang, H. / Schneider, G. / Yu, S.
CitationJournal: Biochem.J. / Year: 2014
Title: Structural and Functional Characterization of Ochratoxinase, a Novel Mycotoxin Degrading Enzyme.
Authors: Dobritzsch, D. / Wang, H. / Schneider, G. / Yu, S.
History
DepositionSep 17, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OCHRATOXINASE
B: OCHRATOXINASE


Theoretical massNumber of molelcules
Total (without water)93,2942
Polymers93,2942
Non-polymers00
Water6,666370
1
A: OCHRATOXINASE
B: OCHRATOXINASE

A: OCHRATOXINASE
B: OCHRATOXINASE

A: OCHRATOXINASE
B: OCHRATOXINASE

A: OCHRATOXINASE
B: OCHRATOXINASE


Theoretical massNumber of molelcules
Total (without water)373,1758
Polymers373,1758
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area35050 Å2
ΔGint-118.9 kcal/mol
Surface area114460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.940, 183.940, 79.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 46 - 480 / Label seq-ID: 4 - 438

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (0.09554, 0.9954, -0.001018), (0.9954, -0.09554, -0.000162), (-0.000258, -0.000998, -1)
Vector: -91.56, 100.7, -74.31)

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Components

#1: Protein OCHRATOXINASE / PROLIDASE


Mass: 46646.828 Da / Num. of mol.: 2
Fragment: EXTRACELLULAR, N-TERMINALLY TRUNCATED ISOFORM, RESIDUES 43-480
Source method: isolated from a genetically manipulated source
Details: 42 RESIDUES TRUNCATED AT N-TERMINUS / Source: (gene. exp.) ASPERGILLUS NIGER (mold) / Strain: UVK143 / Plasmid: PGAPT-OTASE / Production host: ASPERGILLUS NIGER (mold) / Strain (production host): AP4
References: UniProt: A2R2V4, UniProt: G3XP38*PLUS, Xaa-Pro dipeptidase, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CRYSTALLIZED EXTRACELLULAR ISOFORM IS N-TERMINALLY TRUNCATED BY 42 AMINO ACIDS

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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: 3.63 Å3/Da / Density % sol: 66.1 % / Description: NONE
Crystal growpH: 8.5
Details: 10 % (W/V) PEG 3000, 0.1 M TRIS PH 8.5, 0.2 M TRI-POTASSIUM CITRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9762
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: May 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.5→92 Å / Num. obs: 46056 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 9.4
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 3.3 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3BE7, 3FEQ, 2R8C, 3MTW, 2QS8

3be7

3feq

2r8c
PDB Unreleased entry

3mtw

2qs8


Resolution: 2.5→73.28 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 13.928 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.297 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. A 43-44, A 257 AND B 43-45 ARE DISORDERED DISORDERED REGIONS WERE NOT MODELED
RfactorNum. reflection% reflectionSelection details
Rfree0.2089 2380 5.2 %RANDOM
Rwork0.17529 ---
obs0.17704 43557 95.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.077 Å2
Baniso -1Baniso -2Baniso -3
1--2.44 Å20 Å20 Å2
2---2.44 Å20 Å2
3---4.88 Å2
Refinement stepCycle: LAST / Resolution: 2.5→73.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6522 0 0 370 6892
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196671
X-RAY DIFFRACTIONr_bond_other_d0.0030.026385
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.9659057
X-RAY DIFFRACTIONr_angle_other_deg0.943314710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.395869
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48224.139273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.633151067
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9771538
X-RAY DIFFRACTIONr_chiral_restr0.0810.2993
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217666
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021456
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1572.0493479
X-RAY DIFFRACTIONr_mcbond_other1.1572.0493478
X-RAY DIFFRACTIONr_mcangle_it1.9533.074344
X-RAY DIFFRACTIONr_mcangle_other1.9533.074345
X-RAY DIFFRACTIONr_scbond_it1.3542.1943192
X-RAY DIFFRACTIONr_scbond_other1.3542.1943192
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2953.2234712
X-RAY DIFFRACTIONr_long_range_B_refined4.15416.7957899
X-RAY DIFFRACTIONr_long_range_B_other4.06516.6097760
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 25930 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 177 -
Rwork0.263 3234 -
obs--97.6 %
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)
14.90141.7555-1.8271.7817-0.81193.0357-0.0122-0.09970.12860.027-0.05510.11420.0837-0.29540.06730.0997-0.0481-0.03940.067-0.01720.0857-39.200361.468-16.5954
20.13540.24360.20570.43890.36990.45990.0291-0.0065-0.03350.045-0.0065-0.05170.0842-0.018-0.02260.0274-0.01550.00190.02120.00620.1184-15.161875.1077-26.2372
34.4401-0.13131.07677.5013-2.71331.9077-0.0243-0.0308-0.23670.05660.0316-0.47410.16650.0472-0.00730.0722-0.0017-0.02470.0301-0.02510.0722-8.31970.7487-8.3657
42.32840.2921.17061.8039-0.50692.58150.13260.1125-0.227-0.0245-0.0649-0.13580.35510.0851-0.06770.1104-0.02770.02060.0550.00240.0729-23.601657.5161-16.9651
51.88951.62790.68144.54561.26382.8499-0.09860.0176-0.0889-0.08760.06620.07880.282-0.02260.03240.0536-0.02750.00650.08750.04530.073-34.06856.5259-57.5472
60.28120.1592-0.02990.0972-0.07570.54070.03190.0460.07210.01360.03240.03910.0383-0.0416-0.06430.0246-0.01330.00030.0292-0.00520.122-18.282278.5476-48.4106
77.1732-2.22582.12775.4384-2.12661.6413-0.1003-0.2030.64740.0370.12150.2722-0.0709-0.1288-0.02120.0391-0.0249-0.00350.04-0.00910.1213-21.230986.7592-64.5164
81.22160.15650.30582.533-1.5222.9691-0.043-0.05220.16760.09690.13330.3213-0.0979-0.3534-0.09030.045-0.0246-0.02880.0975-0.00670.1637-35.899972.314-58.5375
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A45 - 127
2X-RAY DIFFRACTION2A128 - 247
3X-RAY DIFFRACTION3A248 - 324
4X-RAY DIFFRACTION4A325 - 480
5X-RAY DIFFRACTION5B46 - 128
6X-RAY DIFFRACTION6B129 - 249
7X-RAY DIFFRACTION7B250 - 315
8X-RAY DIFFRACTION8B316 - 480

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