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- PDB-3r09: Crystal structure of probable HAD family hydrolase from Pseudomon... -

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Entry
Database: PDB / ID: 3r09
TitleCrystal structure of probable HAD family hydrolase from Pseudomonas fluorescens Pf-5 with bound Mg
ComponentsHydrolase, haloacid dehalogenase-like family
KeywordsHYDROLASE / structural genomics / enzyme function intitiative / unknown function / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / haloalkane dehalogenase family / possible hydrolase / Enzyme Function Initiative / EFI
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) / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / 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) / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
HAD-superfamily hydrolase, subfamily IA, variant 1 and 3
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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. ...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. / Enzyme Function Initiative (EFI) / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of probable HAD family hydrolase from Pseudomonas fluorescens Pf-5 with bound Mg
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 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Nov 20, 2013Group: Database references / Structure summary
Revision 1.4Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Sep 13, 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
Revision 1.7Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)22,8903
Polymers22,7701
Non-polymers1202
Water2,846158
1
A: Hydrolase, haloacid dehalogenase-like family
hetero molecules

A: Hydrolase, haloacid dehalogenase-like family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7816
Polymers45,5402
Non-polymers2414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area3620 Å2
ΔGint-61 kcal/mol
Surface area17540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.299, 66.299, 251.290
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-212-

HOH

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Components

#1: Protein Hydrolase, haloacid dehalogenase-like family / / Putative HAD family hydrolase


Mass: 22770.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: Pf-5 / ATCC BAA-477 / Gene: PF-5, PFL_5400 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 64.87 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: Protein 10 mM HEPES pH 8.5, 150 mM Nacl, 10% glycerol, 5 mM DTT, 10 mM MgCl2, Reservoir (2.5 M NaK phosphate pH 5.0, 150 mM NaCitrate), Soak (1.5 M MgSO4, 200 mM MES pH 5.3, 20% glycerol, 10 ...Details: Protein 10 mM HEPES pH 8.5, 150 mM Nacl, 10% glycerol, 5 mM DTT, 10 mM MgCl2, Reservoir (2.5 M NaK phosphate pH 5.0, 150 mM NaCitrate), Soak (1.5 M MgSO4, 200 mM MES pH 5.3, 20% glycerol, 10 min, vapor diffusion, sitting drop, temperature 294K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 17605 / Num. obs: 17605 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.1 % / Biso Wilson estimate: 26.5 Å2 / Rsym value: 0.103 / Net I/σ(I): 51.1
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 15.9 % / Mean I/σ(I) obs: 7.8 / Num. unique all: 881 / Rsym value: 0.445 / % possible all: 98.5

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Processing

Software
NameVersionClassificationNB
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
HKL-3000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M9L

3m9l


Resolution: 2.2→32.053 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8727 / SU ML: 0.24 / σ(F): 0 / Phase error: 18.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.208 857 4.98 %random
Rwork0.1791 ---
all0.1806 17198 --
obs0.1806 17198 97.78 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.539 Å2 / ksol: 0.374 e/Å3
Displacement parametersBiso max: 114.03 Å2 / Biso mean: 28.3462 Å2 / Biso min: 9.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.8282 Å20 Å2-0 Å2
2--0.8282 Å2-0 Å2
3----1.6564 Å2
Refinement stepCycle: LAST / Resolution: 2.2→32.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 6 158 1680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061577
X-RAY DIFFRACTIONf_angle_d0.9252157
X-RAY DIFFRACTIONf_chiral_restr0.06242
X-RAY DIFFRACTIONf_plane_restr0.005285
X-RAY DIFFRACTIONf_dihedral_angle_d12.691577
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1997-2.33750.23811300.1942547267795
2.3375-2.51790.26941360.19822605274196
2.5179-2.77110.18811430.18742681282498
2.7711-3.17180.24531440.18382715285999
3.1718-3.9950.20721450.17382797294299
3.995-32.05610.17441590.16892996315599
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)
10.01690.0075-0.0080.0263-0.02140.0162-0.0398-0.01570.0034-0.01870.021-0.00870.0088-0.0005-0.00530.20980.08590.03710.0585-0.00410.102550.50886.024819.5366
20.038-0.0059-0.01370.01130.00250.0056-0.0591-0.01240.0109-0.00250.0295-0.06120.02380.03620.02120.21810.0183-0.04740.0724-0.00120.146865.0748-7.8634-2.2895
30.07720.04620.00470.03450.00240.0333-0.06630.0059-0.05640.01120.05480.01290.0318-0.01350.00290.22950.05320.01360.1160.01410.158252.0637-1.867616.9236
40.0037-0.00340.00640.0032-0.00540.0113-0.0084-0.0074-0.0221-0.0082-0.00320.00810.0032-0.0035-0.01060.16810.0827-0.0440.09530.00240.137243.24517.597420.9798
50.1025-0.0791-0.11610.07620.07570.2163-0.0837-0.0052-0.08520.0116-0.0650.1033-0.0054-0.1120.05110.17550.0461-0.02680.1231-0.04580.208239.16596.781718.8018
60.0137-0.0021-0.00050.01430.00020.0013-0.0279-0.0009-0.0099-0.0578-0.00960.0362-0.0711-0.0252-0.00990.31770.15860.02540.0355-0.02260.099753.155415.821217.4592
70.0548-0.0334-0.01490.0620.02240.0213-0.0087-0.02020.00020.0060.0084-0.0047-0.01190.006-0.00150.20150.09230.02190.16430.01380.136160.83188.211527.4667
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:23)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 24:60)A0
3X-RAY DIFFRACTION3chain 'A' and (resseq 61:85)A0
4X-RAY DIFFRACTION4chain 'A' and (resseq 86:96)A0
5X-RAY DIFFRACTION5chain 'A' and (resseq 97:139)A0
6X-RAY DIFFRACTION6chain 'A' and (resseq 140:187)A0
7X-RAY DIFFRACTION7chain 'A' and (resseq 188:198)A0

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