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- PDB-3m1t: Crystal structure of Putative phosphohydrolase (YP_929327.1) from... -

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Entry
Database: PDB / ID: 3m1t
TitleCrystal structure of Putative phosphohydrolase (YP_929327.1) from Shewanella amazonensis SB2B at 1.62 A resolution
ComponentsPutative phosphohydrolase
KeywordsHYDROLASE / Putative phosphohydrolase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology: / Metal-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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.62 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of Putative phosphohydrolase (YP_929327.1) from Shewanella amazonensis SB2B at 1.62 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 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 / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9572
Polymers29,8651
Non-polymers921
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.729, 69.729, 124.569
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Putative phosphohydrolase / Putative signal transduction protein


Mass: 29865.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella amazonensis (bacteria) / Strain: ATCC BAA-1098 / SB2B / Gene: Sama_3455 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A1SBA1
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT 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: 2.93 Å3/Da / Density % sol: 57.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 1.6000M (NH4)2SO4, 0.1M Bicine pH 9.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97936,0.97925
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 13, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979361
30.979251
ReflectionResolution: 1.62→29.348 Å / Num. obs: 45318 / % possible obs: 100 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 19.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.62-1.667.40.6842.22394932450.68499.6
1.66-1.717.40.5352.92376732190.535100
1.71-1.767.40.4213.72324631450.421100
1.76-1.817.40.334.82249130330.33100
1.81-1.877.40.2646.22190629580.264100
1.87-1.947.40.218.12146228850.21100
1.94-2.017.40.17310.32044027600.173100
2.01-2.097.40.136141984526770.136100
2.09-2.187.40.1118.91891125510.11100
2.18-2.297.40.09621.51814824470.096100
2.29-2.4110.70.11424.92527323700.114100
2.41-2.5612.10.10828.12702522280.108100
2.56-2.7414.40.10133.12989520730.101100
2.74-2.9614.60.0937.42864319620.09100
2.96-3.2414.50.07544.12617418030.075100
3.24-3.6214.50.066492381216450.066100
3.62-4.1814.30.05952.72111814760.059100
4.18-5.12140.0652.11765912590.06100
5.12-7.2413.80.06149.9136229900.061100
7.24-29.3612.20.05250.172035920.05298.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.62→29.348 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 3.386 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.079
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY OTHER REFINEMENT REMARKS: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY OTHER REFINEMENT REMARKS: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.GLYCEROL MOLECULE USED AS CRYOPROTECTANT IS MODELED IN THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.201 2280 5 %RANDOM
Rwork0.182 ---
obs0.183 45270 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 51.09 Å2 / Biso mean: 16.983 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.11 Å20 Å2
2--0.21 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.62→29.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1990 0 6 247 2243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222276
X-RAY DIFFRACTIONr_bond_other_d0.0010.021476
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.9733124
X-RAY DIFFRACTIONr_angle_other_deg1.00533664
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7535318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.12625.68288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.96115390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.93159
X-RAY DIFFRACTIONr_chiral_restr0.10.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212670
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02419
X-RAY DIFFRACTIONr_mcbond_it0.9351.51492
X-RAY DIFFRACTIONr_mcbond_other0.2791.5602
X-RAY DIFFRACTIONr_mcangle_it1.60122416
X-RAY DIFFRACTIONr_scbond_it2.7643784
X-RAY DIFFRACTIONr_scangle_it4.1464.5708
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 156 -
Rwork0.251 3145 -
all-3301 -
obs--99.73 %
Refinement TLS params.Method: refined / Origin x: 37.3784 Å / Origin y: 29.3753 Å / Origin z: 11.5761 Å
111213212223313233
T0.0465 Å2-0.0621 Å20.0012 Å2-0.2006 Å20.0029 Å2--0.0854 Å2
L0.7369 °20.3229 °2-0.2997 °2-0.6419 °20.1206 °2--1.4229 °2
S-0.0392 Å °0.1594 Å °-0.0147 Å °-0.1084 Å °0.0579 Å °0.0257 Å °0.0046 Å °-0.3739 Å °-0.0187 Å °

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