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- PDB-5unq: Crystal Structure of Pt0534 Inactivated by 2-Oxo-3-pentynoate -

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Basic information

Entry
Database: PDB / ID: 5unq
TitleCrystal Structure of Pt0534 Inactivated by 2-Oxo-3-pentynoate
Components(Putative tautomerase) x 2
KeywordsHYDROLASE / 4-Oxalocrotonate tautomerase / MIF / cisCaaD / dehalogenase
Function / homology4-oxalocrotonate tautomerase / Tautomerase enzyme / Tautomerase/MIF superfamily / isomerase activity / Putative tautomerase
Function and homology information
Biological speciesPusillimonas sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.976 Å
AuthorsLeVieux, J. / Baas, B.J. / Zhang, Y.J. / Whitman, C.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-65324 United States
Robert A. Welch FoundationF-1334 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: A global view of structure-function relationships in the tautomerase superfamily.
Authors: Davidson, R. / Baas, B.J. / Akiva, E. / Holliday, G.L. / Polacco, B.J. / LeVieux, J.A. / Pullara, C.R. / Zhang, Y.J. / Whitman, C.P. / Babbitt, P.C.
History
DepositionJan 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Author supporting evidence / Source and taxonomy / Category: entity_src_gen / pdbx_audit_support
Item: _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_audit_support.funding_organization
Revision 1.2Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative tautomerase
B: Putative tautomerase
D: Putative tautomerase
E: Putative tautomerase
F: Putative tautomerase
C: Putative tautomerase


Theoretical massNumber of molelcules
Total (without water)78,8086
Polymers78,8086
Non-polymers00
Water11,620645
1
A: Putative tautomerase
F: Putative tautomerase
C: Putative tautomerase


Theoretical massNumber of molelcules
Total (without water)39,3483
Polymers39,3483
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-30 kcal/mol
Surface area14630 Å2
MethodPISA
2
B: Putative tautomerase
D: Putative tautomerase
E: Putative tautomerase


Theoretical massNumber of molelcules
Total (without water)39,4603
Polymers39,4603
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-32 kcal/mol
Surface area14410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.214, 57.586, 63.528
Angle α, β, γ (deg.)106.69, 104.54, 94.03
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Putative tautomerase


Mass: 13116.015 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pusillimonas sp. (strain T7-7) (bacteria)
Strain: T7-7 / Gene: PT7_0534
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: F4GMX9
#2: Protein Putative tautomerase


Mass: 13228.099 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pusillimonas sp. (strain T7-7) (bacteria)
Strain: T7-7 / Gene: PT7_0534
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: F4GMX9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 645 / 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: 2.32 Å3/Da / Density % sol: 47.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 24% PEG 4000 0.2 M ammonium acetate 0.1 M trisodium citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 47036 / % possible obs: 96 % / Redundancy: 1.8 % / Net I/σ(I): 6.63

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N4G

3n4g


Resolution: 1.976→40.83 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2556 2289 4.87 %
Rwork0.2119 --
obs0.2141 47016 95.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.976→40.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5492 0 0 645 6137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025570
X-RAY DIFFRACTIONf_angle_d0.537510
X-RAY DIFFRACTIONf_dihedral_angle_d11.9172094
X-RAY DIFFRACTIONf_chiral_restr0.019868
X-RAY DIFFRACTIONf_plane_restr0.002981
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9756-2.01860.3541290.29192147X-RAY DIFFRACTION74
2.0186-2.06550.29951280.27382641X-RAY DIFFRACTION89
2.0655-2.11720.34331440.27762736X-RAY DIFFRACTION94
2.1172-2.17440.30261530.25992780X-RAY DIFFRACTION95
2.1744-2.23840.29811610.26572809X-RAY DIFFRACTION97
2.2384-2.31070.32821280.25942829X-RAY DIFFRACTION96
2.3107-2.39320.31211370.24562883X-RAY DIFFRACTION97
2.3932-2.4890.31341440.23682874X-RAY DIFFRACTION97
2.489-2.60230.28361510.23162842X-RAY DIFFRACTION97
2.6023-2.73950.30821550.23812867X-RAY DIFFRACTION98
2.7395-2.91110.27471540.21892877X-RAY DIFFRACTION98
2.9111-3.13580.29441350.22242864X-RAY DIFFRACTION98
3.1358-3.45120.22841450.20952895X-RAY DIFFRACTION98
3.4512-3.95020.2031480.18242872X-RAY DIFFRACTION98
3.9502-4.97550.19311580.1522880X-RAY DIFFRACTION98
4.9755-40.83870.21321190.18672931X-RAY DIFFRACTION99
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)
10.03830.0909-0.00930.0709-0.02250.02740.0554-0.0703-0.1548-0.11370.046-0.0236-0.1418-0.04100.09290.0136-0.01660.10310.00530.1186-32.1802-7.5645-80.6899
20.00360.0015-0.0068-0.00050.00480.00140.06980.0288-0.03420.04270.10270.0031-0.06440.045-00.17830.013-0.00860.17680.00020.1687-46.35663.0066-85.1589
3-0.0096-0.04630.00840.01570.05210.01360.075-0.1351-0.00370.0031-0.02430.0945-0.17190.003600.1106-0.0118-0.02340.1846-0.00760.1133-36.93023.2881-76.5298
40.02830.0182-0.02610.09650.10530.0501-0.0905-0.01470.01110.02290.0368-0.1722-0.0619-0.094800.14440.0112-0.020.17920.01370.1728-30.6811.5279-74.2094
50.00010.00130.0040.0088-0.0110.005-0.003-0.0158-0.03320.0887-0.1684-0.00370.03060.054200.1827-0.0056-0.01570.14190.0490.1801-34.0813-13.4467-56.8108
60.0004-0.0542-0.02790.06270.03260.0334-0.10590.02040.08210.01150.0719-0.0783-0.0882-0.0627-00.1137-0.01850.0160.12690.00680.0915-48.4276-5.7157-108.7689
70.0057-0.0061-0.02160.00440.00510.0272-0.005-0.0021-0.10070.2537-0.06110.0301-0.13440.0503-00.10430.01730.00640.1836-0.020.1669-47.2233-19.1308-97.5266
80.0124-0.0172-0.0023-0.00180.00380.0063-0.02840.16050.02180.02680.15890.20010.1198-0.076-00.1334-0.0084-0.01940.3157-0.1419-0.2673-56.6592-14.4019-116.5698
90.03490.070.0090.05320.09870.04150.17270.11080.0143-0.1-0.08080.0120.04080.0406-00.11580.00170.04450.16920.00070.1396-54.6018-12.6-114.7698
100.0588-0.02890.10140.1809-0.0870.20780.04420.0833-0.05140.093-0.0249-0.0122-0.0394-0.039900.1182-0.00020.01280.1297-0.03120.1176-66.9242-6.7573-97.4076
110.0041-0.01810.01870.00330.0261-0.02280.0878-0.0173-0.0143-0.2039-0.0631-0.05390.0723-0.0131-00.15770.0219-0.03380.1503-0.02840.1949-72.9059-15.9258-108.2075
12-0.0209-0.00340.0650.03390.01930.0827-0.0254-0.0551-0.0139-0.10570.0356-0.02230.0307-0.020200.1465-0.0107-0.03910.156-0.03090.1867-72.5131-13.707-105.51
130.1337-0.0905-0.0460.07360.06390.1406-0.1085-0.02740.0162-0.01340.1121-0.0349-0.0348-0.0327-00.13020.0166-0.00460.1459-0.02350.1223-54.41865.7052-77.8733
14-0.01020.0210.010.0019-0.00640.0031-0.0432-0.0618-0.11450.10010.0776-0.0310.06940.077100.11770.0013-0.02650.1945-0.0260.143-45.065811.6719-67.4103
15-0.0147-0.0239-0.01090.13940.09180.0968-0.0456-0.07060.09470.0091-0.03510.023-0.06570.0045-00.12590.0022-0.03310.1452-0.02280.1455-47.388311.3588-69.9797
160.0383-0.06330.0899-0.02910.05880.01970.0332-0.0412-0.0485-0.086-0.06420.0349-0.1204-0.126200.13680.02490.00320.15850.02230.1244-54.5313-12.1409-68.0937
170.0737-0.07810.08640.0126-0.03190.03960.0570.1309-0.24060.13690.0414-0.10880.09630.0364-00.1783-0.02260.02760.05080.07690.0133-44.2293-12.6136-65.3642
18-0.0543-0.0259-0.0184-0.0036-0.02280.0194-0.0097-0.3830.04990.1963-0.001-0.04770.208-0.277100.15910.0181-0.00260.143-0.01430.138-48.8342-0.6369-61.1892
190.07270.02920.03180.00610.02920.00230.1218-0.0373-0.1418-0.0369-0.0174-0.0099-0.00260.045700.1481-0.0003-0.02320.10330.03310.1709-54.9106-28.7672-93.1508
200.0014-0.00620.00250.00210.0019-0.001-0.09580.0778-0.0022-0.0617-0.0361-0.0147-0.01230.06340-0.17790.73960.3984-0.7053-0.452-0.1069-48.1608-31.433-104.2304
210.0035-0.00480.00290.01460.0038-0.0036-0.0553-0.0196-0.09080.20120.051-0.1165-0.0198-0.0494-00.1884-0.02210.02350.14320.03620.116-65.185-17.0748-90.0216
22-0.0163-0.0187-0.01020.06650.0252-0.00230.1203-0.25920.0061-0.10510.0704-0.15730.1844-0.036500.1666-0.0127-0.00350.03680.03780.1152-62.1049-32.5433-101.6127
23-0.00720.04880.0193-0.01820.00770.00770.01710.179-0.16410.02990.03880.1544-0.00140.010500.1556-0.0010.02210.13490.00990.1767-65.7852-27.055-99.9705
240.0034-0.00820.006-0.0016-0.00010.0010.2647-0.0398-0.015-0.04950.28680.25450.0037-0.00930-0.02180.15990.27950.2857-0.3974-0.2043-49.3117-23.6525-116.0934
250.0051-0.00060.00110.00640.00370.0027-0.07170.0041-0.04580.0227-0.0114-0.0030.095-0.0245-00.23260.04230.01660.4712-0.13940.1779-48.8504-28.8618-119.3396
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 3:42 )B3 - 42
2X-RAY DIFFRACTION2( CHAIN B AND RESID 43:52 )B43 - 52
3X-RAY DIFFRACTION3( CHAIN B AND RESID 53:72 )B53 - 72
4X-RAY DIFFRACTION4( CHAIN B AND RESID 73:112 )B73 - 112
5X-RAY DIFFRACTION5( CHAIN B AND RESID 113:123 )B113 - 123
6X-RAY DIFFRACTION6( CHAIN A AND RESID 2:39 )A2 - 39
7X-RAY DIFFRACTION7( CHAIN A AND RESID 40:61 )A40 - 61
8X-RAY DIFFRACTION8( CHAIN A AND RESID 62:73 )A62 - 73
9X-RAY DIFFRACTION9( CHAIN A AND RESID 74:123 )A74 - 123
10X-RAY DIFFRACTION10( CHAIN C AND RESID 2:61 )C2 - 61
11X-RAY DIFFRACTION11( CHAIN C AND RESID 62:73 )C62 - 73
12X-RAY DIFFRACTION12( CHAIN C AND RESID 74:122 )C74 - 122
13X-RAY DIFFRACTION13( CHAIN D AND RESID 2:61 )D2 - 61
14X-RAY DIFFRACTION14( CHAIN D AND RESID 62:73 )D62 - 73
15X-RAY DIFFRACTION15( CHAIN D AND RESID 74:122 )D74 - 122
16X-RAY DIFFRACTION16( CHAIN E AND RESID 2:46 )E2 - 46
17X-RAY DIFFRACTION17( CHAIN E AND RESID 47:92 )E47 - 92
18X-RAY DIFFRACTION18( CHAIN E AND RESID 93:123 )E93 - 123
19X-RAY DIFFRACTION19( CHAIN F AND RESID 2:32 )F2 - 32
20X-RAY DIFFRACTION20( CHAIN F AND RESID 33:39 )F33 - 39
21X-RAY DIFFRACTION21( CHAIN F AND RESID 40:61 )F40 - 61
22X-RAY DIFFRACTION22( CHAIN F AND RESID 62:92 )F62 - 92
23X-RAY DIFFRACTION23( CHAIN F AND RESID 93:106 )F93 - 106
24X-RAY DIFFRACTION24( CHAIN F AND RESID 107:116 )F107 - 116
25X-RAY DIFFRACTION25( CHAIN F AND RESID 117:123 )F117 - 123

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