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- PDB-3i7a: Crystal structure of Putative metal-dependent phosphohydrolase (Y... -

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Basic information

Entry
Database: PDB / ID: 3i7a
TitleCrystal structure of Putative metal-dependent phosphohydrolase (YP_926882.1) from Shewanella amazonensis SB2B at 2.06 A resolution
ComponentsPutative metal-dependent phosphohydrolase
KeywordsHYDROLASE / YP_926882.1 / Putative metal-dependent phosphohydrolase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyMetal-dependent hydrolase HDOD / HDOD domain / HD-related output (HDOD) domain profile. / Hypothetical protein af1432 / Hypothetical protein af1432 / Orthogonal Bundle / Mainly Alpha / Putative signal transduction protein
Function and homology information
Biological speciesShewanella amazonensis SB2B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.06 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative metal-dependent phosphohydrolase (YP_926882.1) from Shewanella amazonensis SB2B at 2.06 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative metal-dependent phosphohydrolase


Theoretical massNumber of molelcules
Total (without water)31,3671
Polymers31,3671
Non-polymers00
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.626, 76.626, 57.783
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Putative metal-dependent phosphohydrolase / Putative signal transduction protein


Mass: 31366.627 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella amazonensis SB2B (bacteria) / Gene: Sama_1005, YP_926882.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A1S4A6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 1-280) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 1-280) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.7 Å3/Da / Density % sol: 54.51 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND .
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20.0000% PEG-6000, 0.1M TRIS pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91162,0.97839,0.97799
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 16, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.978391
30.977991
ReflectionResolution: 2.06→29.476 Å / Num. obs: 20761 / % possible obs: 98 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 29.504 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 11.62
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.06-2.140.4081.973873843198.3
2.14-2.230.3182.579844139198.5
2.23-2.330.2393.476183950198.3
2.33-2.450.1694.675443896198.6
2.45-2.610.145.781004173198.5
2.61-2.810.1037.776973958198.5
2.81-3.090.0691177783992198.5
3.09-3.530.04117.276153891197.6
3.53-4.440.02527.877323943196.8
4.44-29.4760.01934.778493985196.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.06→29.476 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 9.235 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.171
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1067 5.1 %RANDOM
Rwork0.185 ---
obs0.188 20740 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.72 Å2 / Biso mean: 26.543 Å2 / Biso min: 8.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2--0.33 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 2.06→29.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2157 0 0 138 2295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222257
X-RAY DIFFRACTIONr_bond_other_d0.0010.021495
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.9723085
X-RAY DIFFRACTIONr_angle_other_deg0.97433680
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9855296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.76424.37596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87215391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5441514
X-RAY DIFFRACTIONr_chiral_restr0.0880.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212521
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02433
X-RAY DIFFRACTIONr_mcbond_it1.91731423
X-RAY DIFFRACTIONr_mcbond_other0.533572
X-RAY DIFFRACTIONr_mcangle_it3.0252310
X-RAY DIFFRACTIONr_scbond_it5.6488834
X-RAY DIFFRACTIONr_scangle_it7.81111766
LS refinement shellResolution: 2.06→2.115 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 77 -
Rwork0.225 1446 -
all-1523 -
obs--99.61 %
Refinement TLS params.Method: refined / Origin x: 12.6305 Å / Origin y: 28.8356 Å / Origin z: 29.1566 Å
111213212223313233
T0.0348 Å20.0118 Å20.0154 Å2-0.0399 Å20.0179 Å2--0.0258 Å2
L1.2445 °2-0.6504 °20.0422 °2-1.0855 °20.1817 °2--0.3832 °2
S-0.0192 Å °-0.0003 Å °0.0095 Å °0.023 Å °-0.046 Å °-0.0618 Å °0.0406 Å °0.0174 Å °0.0652 Å °

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