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- PDB-5uif: Crystal Structure of Native Ps01740 -

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Basic information

Entry
Database: PDB / ID: 5uif
TitleCrystal Structure of Native Ps01740
ComponentsPs01740
KeywordsHYDROLASE / 4-oxalocrotonate-Tautomerase / MIF / cis-Caad / dehalogenase
Function / homology: / Tautomerase, cis-CaaD-like / Putative oxalocrotonate tautomerase enzyme / Tautomerase/MIF superfamily / Tautomerase_3 domain-containing protein
Function and homology information
Biological speciesPseudomonas sp. UW4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 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: Arch. Biochem. Biophys. / Year: 2017
Title: Kinetic and structural characterization of a cis-3-Chloroacrylic acid dehalogenase homologue in Pseudomonas sp. UW4: A potential step between subgroups in the tautomerase superfamily.
Authors: LeVieux, J.A. / Baas, B.J. / Kaoud, T.S. / Davidson, R. / Babbitt, P.C. / Zhang, Y.J. / Whitman, C.P.
History
DepositionJan 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 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 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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

Downloads & links

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Assembly

Deposited unit
A: Ps01740
B: Ps01740
C: Ps01740


Theoretical massNumber of molelcules
Total (without water)40,6483
Polymers40,6483
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-29 kcal/mol
Surface area13480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.722, 58.902, 84.759
Angle α, β, γ (deg.)90.00, 110.37, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ps01740


Mass: 13549.295 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. UW4 (bacteria) / Gene: PputUW4_01740
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: K9NIA5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 47.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 18% PEG 8000 0.1 M CHES pH 9.0 / Temp details: room temperature

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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: 2.57→46.48 Å / Num. obs: 11402 / % possible obs: 96 % / Redundancy: 3.5 % / Net I/σ(I): 7.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N4G

3n4g


Resolution: 2.57→46.48 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.81
RfactorNum. reflection% reflection
Rfree0.2716 584 5.12 %
Rwork0.2192 --
obs0.2218 11402 95.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.57→46.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2520 0 0 57 2577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022565
X-RAY DIFFRACTIONf_angle_d0.4643495
X-RAY DIFFRACTIONf_dihedral_angle_d13.052924
X-RAY DIFFRACTIONf_chiral_restr0.018420
X-RAY DIFFRACTIONf_plane_restr0.002450
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5739-2.83290.41131240.30252279X-RAY DIFFRACTION81
2.8329-3.24270.29841670.27382795X-RAY DIFFRACTION99
3.2427-4.08510.24391440.21732846X-RAY DIFFRACTION100
4.0851-46.48840.24461490.18072898X-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)
14.33790.0785-0.78455.2382-1.07483.11880.03830.08470.0234-0.1008-0.1798-0.30060.17420.41010.13660.39940.03840.06990.6103-0.02240.31447.648323.25268.652
27.38561.0096-2.0261.1541-1.16531.9112-0.58580.8584-1.3487-0.0960.1061-0.01350.3397-0.19220.40970.393-0.0767-0.01470.3556-0.10470.3605-4.145217.944919.2687
32.51431.0205-0.55757.69050.8986.0831-0.26040.12310.20490.112-0.0268-0.1876-0.1806-0.12620.53520.36390.03640.00490.45340.05810.27921.844631.79928.8916
45.02020.9612.36993.47461.81057.2831-0.3480.1180.96760.026-0.188-0.086-0.34070.07320.45920.38610.1109-0.00060.40340.13390.47754.230131.841515.9714
58.3411-4.82912.49015.6256-2.24722.7018-0.1506-0.1852-0.356-1.0260.3239-0.86080.9296-0.16820.01310.37020.0380.07660.40450.01290.5485-3.451919.800930.0588
66.6462-3.48371.40672.6403-2.315.62790.41080.2741-0.0712-0.4633-0.67120.70030.4483-0.54580.22880.3159-0.0160.08880.601-0.00790.4658-14.524524.015930.2404
73.4892-4.07184.13186.7695-2.64077.88620.31042.4163-1.2517-0.4084-0.42090.5562-0.06520.9639-0.05360.3502-0.0910.06590.51830.03930.4003-8.973824.298123.4243
88.33874.4102-3.55515.6823-1.99236.31911.274-2.2666-0.90350.3531-1.222-0.99580.62540.1664-0.29830.5490.1133-0.00030.44160.27920.48849.00316.886338.0359
91.88751.1356-2.10179.6734-2.59997.2325-0.09940.0560.5374-1.46750.0689-0.42390.24090.17150.01980.3406-0.07950.01530.49070.07260.5931-5.037933.808726.6998
101.9199-1.40051.12913.1273-4.86726.2964-0.3716-0.48580.21530.49350.1666-1.1826-0.195-0.05960.48120.28120.027-0.00860.49490.01770.5188-9.384730.871237.1139
112.68242.0653-2.76644.8187-1.11397.3926-0.4507-1.04450.5148-0.2539-1.1421-0.20080.91581.35251.33070.3680.04340.00640.49540.05990.5538-2.091129.189835.9729
122.61212.18342.55017.88254.06263.12810.92570.7478-0.1353-0.3601-0.55280.3123-1.0711-0.8465-0.45930.62490.1536-0.02310.7728-0.11440.744-3.771336.645614.0743
134.18030.31062.25091.8952-1.35615.6035-0.0745-0.6545-0.11110.31290.0207-0.04160.2881-0.16920.01850.2550.11910.01540.46540.02990.456914.696521.291829.4169
149.6-3.7742-2.45019.24962.23844.3775-0.4854-0.56140.30650.7638-0.39261.42180.0506-0.68080.7630.33280.0483-0.06830.58290.06610.73911.371733.933130.4898
154.40020.00031.8885.60140.45472.11360.076-0.0793-0.0095-0.1644-0.0763-0.4019-0.25520.28550.00890.31740.0168-0.00250.47390.07930.353316.720131.228628.4214
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:40 )A2 - 40
2X-RAY DIFFRACTION2( CHAIN A AND RESID 41:61 )A41 - 61
3X-RAY DIFFRACTION3( CHAIN A AND RESID 62:92 )A62 - 92
4X-RAY DIFFRACTION4( CHAIN A AND RESID 93:112 )A93 - 112
5X-RAY DIFFRACTION5( CHAIN B AND RESID 2:14 )B2 - 14
6X-RAY DIFFRACTION6( CHAIN B AND RESID 15:33 )B15 - 33
7X-RAY DIFFRACTION7( CHAIN B AND RESID 34:47 )B34 - 47
8X-RAY DIFFRACTION8( CHAIN B AND RESID 48:61 )B48 - 61
9X-RAY DIFFRACTION9( CHAIN B AND RESID 62:73 )B62 - 73
10X-RAY DIFFRACTION10( CHAIN B AND RESID 74:92 )B74 - 92
11X-RAY DIFFRACTION11( CHAIN B AND RESID 93:106 )B93 - 106
12X-RAY DIFFRACTION12( CHAIN B AND RESID 107:112 )B107 - 112
13X-RAY DIFFRACTION13( CHAIN C AND RESID 2:61 )C2 - 61
14X-RAY DIFFRACTION14( CHAIN C AND RESID 62:73 )C62 - 73
15X-RAY DIFFRACTION15( CHAIN C AND RESID 74:112 )C74 - 112

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