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- PDB-2ybd: Crystal structure of probable had family hydrolase from pseudomon... -

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Basic information

Entry
Database: PDB / ID: 2ybd
TitleCrystal structure of probable had family hydrolase from pseudomonas fluorescens pf-5 with bound phosphate
ComponentsHYDROLASE, HALOACID DEHALOGENASE-LIKE FAMILY
KeywordsHYDROLASE / PSI
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
434 Repressor (Amino-terminal Domain) - #80 / Haloacid dehalogenase-like hydrolase / HAD hydrolase, subfamily IA / 434 Repressor (Amino-terminal Domain) / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / Rossmann fold / Orthogonal Bundle ...434 Repressor (Amino-terminal Domain) - #80 / Haloacid dehalogenase-like hydrolase / HAD hydrolase, subfamily IA / 434 Repressor (Amino-terminal Domain) / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / HAD-superfamily hydrolase, subfamily IA, variant 1 and 3
Similarity search - Component
Biological speciesPSEUDOMONAS FLUORESCENS PF-5 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsVetting, M.W. / Patskovsky, Y. / Toro, R. / Freeman, J. / Miller, S. / Sauder, J.M. / Burley, S.K. / Dunaway-Mariano, D. / Allen, K.N. / Gerlt, J.A. / Almo, S.C.
CitationJournal: To be Published
Title: Crystal Structure of Probable Had Family Hydrolase from Pseudomonas Fluorescens Pf-5 with Bound Phosphate
Authors: Vetting, M.W. / Patskovsky, Y. / Toro, R. / Freeman, J. / Miller, S. / Sauder, J.M. / Burley, S.K. / Dunaway-Mariano, D. / Allen, K.N. / Gerlt, J.A. / Almo, S.C.
History
DepositionMar 3, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_database_status / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 20, 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: HYDROLASE, HALOACID DEHALOGENASE-LIKE FAMILY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9844
Polymers22,7701
Non-polymers2143
Water4,125229
1
A: HYDROLASE, HALOACID DEHALOGENASE-LIKE FAMILY
hetero molecules

A: HYDROLASE, HALOACID DEHALOGENASE-LIKE FAMILY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9698
Polymers45,5402
Non-polymers4286
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area4100 Å2
ΔGint-67.6 kcal/mol
Surface area17350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.978, 65.978, 250.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-2103-

HOH

21A-2185-

HOH

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Components

#1: Protein HYDROLASE, HALOACID DEHALOGENASE-LIKE FAMILY


Mass: 22770.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS FLUORESCENS PF-5 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q4K5L5
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 3.5 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growpH: 5
Details: PROTEIN (10MM HEPES PH 7.5, 150 MM NACL, 10% GLYCEROL, 5 MM DTT, 5 MM MGCL);RESERVOUR (2.5 M NA/K PHOSPHATE, 150 MM NACITRATE, PH 5.0;CRYOPROTECTION (1.8 M NA/K PHOSPHATE, 100 MM NACITRATE, ...Details: PROTEIN (10MM HEPES PH 7.5, 150 MM NACL, 10% GLYCEROL, 5 MM DTT, 5 MM MGCL);RESERVOUR (2.5 M NA/K PHOSPHATE, 150 MM NACITRATE, PH 5.0;CRYOPROTECTION (1.8 M NA/K PHOSPHATE, 100 MM NACITRATE, 18.5% GLYCEROL, 185 MM MGSO4) TWO MINUTE SOAK.

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU-MSC RAXIS IV / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 22605 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 15.3 % / Biso Wilson estimate: 22.11 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 32.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 6.4 / % possible all: 89.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M9L

3m9l


Resolution: 2.001→32.989 Å / SU ML: 0.22 / σ(F): 0 / Phase error: 17.96 / Stereochemistry target values: ML
Details: MAGNESIUM IN ACTIVE SITE CHOSEN OVER WATER DUE TO COORDINATION NUMBER AND GEOMETRY. MOST LIKELY DOES NOT REPRESENT THE TYPICAL COORDINATION DURING CHEMISTRY. PHOSPHATE IS ASSUMED TO BE BOUND ...Details: MAGNESIUM IN ACTIVE SITE CHOSEN OVER WATER DUE TO COORDINATION NUMBER AND GEOMETRY. MOST LIKELY DOES NOT REPRESENT THE TYPICAL COORDINATION DURING CHEMISTRY. PHOSPHATE IS ASSUMED TO BE BOUND BY THE ACTIVE SITE POSITION THAT COORDINATES THE PHOSPHATE OF SUBSTRATE.
RfactorNum. reflection% reflection
Rfree0.2177 1106 5.1 %
Rwork0.1707 --
obs0.173 21908 95.89 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.422 Å2 / ksol: 0.376 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.8479 Å20 Å20 Å2
2--0.8479 Å20 Å2
3----1.6957 Å2
Refinement stepCycle: LAST / Resolution: 2.001→32.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1507 0 11 229 1747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081591
X-RAY DIFFRACTIONf_angle_d1.0322180
X-RAY DIFFRACTIONf_dihedral_angle_d11.246582
X-RAY DIFFRACTIONf_chiral_restr0.071244
X-RAY DIFFRACTIONf_plane_restr0.005288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0009-2.09190.28131250.21622221X-RAY DIFFRACTION85
2.0919-2.20220.21011320.16972479X-RAY DIFFRACTION93
2.2022-2.34010.24081350.16592523X-RAY DIFFRACTION96
2.3401-2.52080.21591370.16582570X-RAY DIFFRACTION97
2.5208-2.77430.20931360.16572634X-RAY DIFFRACTION98
2.7743-3.17550.22561420.16532680X-RAY DIFFRACTION99
3.1755-3.99970.19021450.16522740X-RAY DIFFRACTION100
3.9997-32.99350.22371540.17542955X-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)
10.24860.1412-0.0290.3281-0.07710.023-0.17630.1446-0.0196-0.09440.14450.045-0.043-0.05380.01610.19260.1160.0008-0.05720.04440.091550.43356.173419.3473
20.0946-0.0174-0.05440.0391-0.05060.1035-0.1496-0.0090.00070.05280.0713-0.13070.05740.07930.0150.18610.0172-0.04240.0883-0.00120.121865.0061-7.8637-2.2223
30.0809-0.0222-0.08510.0229-0.01670.1088-0.106-0.0214-0.08190.05010.0120.0870.1381-0.09450.00880.17210.02520.00570.08730.01380.111451.7545-1.932916.8401
40.062-0.00610.01260.03680.06930.1984-0.15540.0708-0.14450.0087-0.05090.0786-0.0135-0.03770.02830.18850.0469-0.00980.147-0.01650.160443.11748.044320.5064
50.1405-0.1274-0.03280.09980.04980.1024-0.0640.0039-0.13230.09470.00680.3439-0.0613-0.31630.01810.1830.0504-0.01550.1019-0.02570.195539.17048.543219.5103
60.08980.0193-0.03320.0143-0.01230.0648-0.0168-0.0659-0.0314-0.06780.01420.0182-0.20790.02850.00480.18520.04980.01780.07190.0050.08855.743514.112518.3558
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESSEQ 2:23)
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESSEQ 24:60)
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESSEQ 61:85)
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESSEQ 86:96)
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESSEQ 97:143)
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESSEQ 144:197)

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