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- PDB-4c5y: Crystal structure of A. niger ochratoxinase -

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Basic information

Entry
Database: PDB / ID: 4c5y
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 ...: / 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
Biological speciesASPERGILLUS NIGER (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 1.2Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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 / _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

Downloads & links

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Assembly

Deposited unit
A: OCHRATOXINASE
B: OCHRATOXINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,6416
Polymers93,3802
Non-polymers2624
Water55831
1
A: OCHRATOXINASE
B: OCHRATOXINASE
hetero molecules

A: OCHRATOXINASE
B: OCHRATOXINASE
hetero molecules

A: OCHRATOXINASE
B: OCHRATOXINASE
hetero molecules

A: OCHRATOXINASE
B: OCHRATOXINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)374,56524
Polymers373,5198
Non-polymers1,04716
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 area37660 Å2
ΔGint-749 kcal/mol
Surface area110270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.240, 183.240, 78.980
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: ASP / Beg label comp-ID: ASP / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 45 - 480 / Label seq-ID: 3 - 438

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

NCS oper: (Code: given
Matrix: (0.1101, 0.9939, 0.000983), (0.9939, -0.1101, -0.000319), (-0.000209, 0.001012, -1)
Vector: -91.07, 101.8, -74.08)

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Components

#1: Protein OCHRATOXINASE / PROLIDASE


Mass: 46689.828 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, Xaa-Pro dipeptidase, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 3.56 Å3/Da / Density % sol: 65.4 % / Description: NONE
Crystal growpH: 9
Details: 12% (W/V) PEG 3000, 0.1 M BICINE PH 9.0, 0.2 M TRI-POTASSIUM CITRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3→72.5 Å / Num. obs: 26324 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 6.3
Reflection shellResolution: 3→3.16 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.2 / % possible all: 97.2

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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: 3→67.44 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.914 / SU B: 34.251 / SU ML: 0.277 / Cross valid method: THROUGHOUT / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED RESIDUES A 43,A 44, B 43,B 44, B 349-351. DISORDERED REGIONS WERE NOT MODELED. RESIDUES 334-353 ADOPT DUAL CONFORMATIONS IN BOTH ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED RESIDUES A 43,A 44, B 43,B 44, B 349-351. DISORDERED REGIONS WERE NOT MODELED. RESIDUES 334-353 ADOPT DUAL CONFORMATIONS IN BOTH CHAINS, ONLY THE PREDOMINANT ONE WAS MODELED
RfactorNum. reflection% reflectionSelection details
Rfree0.22583 1341 5.1 %RANDOM
Rwork0.18801 ---
obs0.18999 24926 95.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.349 Å2
Baniso -1Baniso -2Baniso -3
1--1.55 Å20 Å20 Å2
2---1.55 Å20 Å2
3---3.11 Å2
Refinement stepCycle: LAST / Resolution: 3→67.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6516 0 4 31 6551
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196671
X-RAY DIFFRACTIONr_bond_other_d0.0040.026358
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.9689036
X-RAY DIFFRACTIONr_angle_other_deg0.992314649
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2235866
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.07924.176273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.607151055
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7461538
X-RAY DIFFRACTIONr_chiral_restr0.0750.2991
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217656
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021450
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_it1.5153.2783473
X-RAY DIFFRACTIONr_mcbond_other1.5153.2783472
X-RAY DIFFRACTIONr_mcangle_it2.5294.9154336
X-RAY DIFFRACTIONr_mcangle_other2.5294.9154337
X-RAY DIFFRACTIONr_scbond_it1.7373.4663198
X-RAY DIFFRACTIONr_scbond_other1.7363.4663197
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7685.1164700
X-RAY DIFFRACTIONr_long_range_B_refined5.38531.32128521
X-RAY DIFFRACTIONr_long_range_B_other5.38331.32228517
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 25431 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 99 -
Rwork0.306 1845 -
obs--97.25 %
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)
10.95121.091-0.18761.6707-0.32662.2850.0714-0.10060.00320.192-0.19810.23090.3203-0.52970.12670.268-0.18530.08710.2225-0.11060.1776-33.46364.6994-21.0411
21.315-0.54870.09410.25640.28243.83840.02640.0088-0.32390.0131-0.02930.13260.4308-0.0340.00290.1093-0.03750.07790.0269-0.03480.2339-7.821778.7333-23.5361
33.74350.09691.66563.9726-1.54722.3903-0.0118-0.2464-0.2870.2984-0.0148-0.21520.3053-0.0190.02660.265-0.03530.07630.1118-0.04560.0978-9.67569.5905-8.3875
40.03210.14850.03651.30090.38310.1188-0.33540.117-0.0303-0.12150.7268-0.69430.04360.2991-0.39141.22370.0796-0.00311.0807-0.01381.0508-3.93252.456-22.1802
51.87181.92141.04452.04721.10872.5044-0.17230.06510.0319-0.22050.070.14010.2866-0.32680.10230.1777-0.14720.00130.2399-0.0340.2186-30.64861.0789-52.9616
60.0338-0.0393-0.30711.34890.31483.2004-0.04140.03980.007-0.04150.0160.3151-0.0731-0.50840.02540.0851-0.00040.01210.1415-0.08550.2608-14.173585.6053-50.4812
74.8614-0.9081.40462.9208-1.38012.1916-0.0887-0.04010.3535-0.0740.10690.4944-0.0099-0.3876-0.01820.1159-0.0754-0.00530.1442-0.02590.1546-25.349584.9079-63.8227
82.9033-2.8559-3.25516.55382.99513.66110.74160.28960.47640.0348-0.2001-0.4685-0.8715-0.3325-0.54150.39640.01690.03820.5139-0.01850.3606-37.513794.4963-56.6414
92.47290.46110.66261.7472-0.02132.52690.0863-0.1317-0.37460.1883-0.19580.1170.6841-0.15730.10960.3695-0.22480.11280.208-0.04860.139-25.137557.3153-11.6758
102.1252.13670.65354.3195-0.31433.46930.11810.14220.02730.2195-0.35390.50340.282-0.51850.23590.2619-0.24640.10290.4819-0.19450.2626-39.18962.6029-29.836
111.91860.985-0.49661.8376-0.49962.2974-0.10880.17980.1017-0.0760.16190.48640.2111-0.6237-0.05310.1345-0.1563-0.03560.3192-0.02990.2584-37.018270.0953-62.1757
124.56942.2011-1.0471.6230.9964.2476-0.11210.13210.03460.1869-0.06230.09820.5949-0.25810.17430.3436-0.19680.05670.2125-0.04430.234-32.874755.5209-44.0898
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A45 - 185
2X-RAY DIFFRACTION2A186 - 254
3X-RAY DIFFRACTION3A255 - 333
4X-RAY DIFFRACTION4A334 - 354
5X-RAY DIFFRACTION5B45 - 183
6X-RAY DIFFRACTION6B184 - 256
7X-RAY DIFFRACTION7B257 - 346
8X-RAY DIFFRACTION8B347 - 355
9X-RAY DIFFRACTION9A355 - 448
10X-RAY DIFFRACTION10A449 - 480
11X-RAY DIFFRACTION11B356 - 449
12X-RAY DIFFRACTION12B450 - 480

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