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- PDB-3bhn: Crystal structure of a dj-1/pfpi-like protein (shew_2856) from sh... -

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Basic information

Entry
Database: PDB / ID: 3bhn
TitleCrystal structure of a dj-1/pfpi-like protein (shew_2856) from shewanella loihica pv-4 at 1.76 A resolution
ComponentsThiJ/PfpI domain protein
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology: / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / ThiJ/PfpI domain protein
Function and homology information
Biological speciesShewanella loihica PV-4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.76 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of DJ-1 like Protein (YP_001094981.1) from Shewanella loihica PV-4 at 1.76 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 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 1.4Jan 25, 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
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ThiJ/PfpI domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5764
Polymers26,3901
Non-polymers1863
Water3,675204
1
A: ThiJ/PfpI domain protein
hetero molecules

A: ThiJ/PfpI domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1528
Polymers52,7802
Non-polymers3726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_575x,x-y+2,-z+1/61
Buried area2610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.320, 71.320, 180.630
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein ThiJ/PfpI domain protein


Mass: 26389.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella loihica PV-4 (bacteria) / Species: Shewanella loihica / Strain: PV-4, BAA-1088 / Gene: YP_001094981.1, Shew_2856 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A3QGX4
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsREMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG.

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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: 2.51 Å3/Da / Density % sol: 51.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: NANODROP, 0.2M Na Tartrate, 20.0% PEG 3350, No Buffer pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537, 0.9798, 0.9796
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 4, 2007
RadiationMonochromator: Double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.97981
30.97961
ReflectionResolution: 1.76→29.223 Å / Num. obs: 27863 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 10.35 % / Biso Wilson estimate: 22.32 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.14
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsDiffraction-ID% possible all
1.76-1.820.806226238195.4
1.82-1.90.62.8316361100
1.9-1.980.436426930199.9
1.98-2.090.296.1305811100
2.09-2.220.1938.8287681100
2.22-2.390.13911.8287981100
2.39-2.630.10115.3291621100
2.63-3.010.0722028919199.9
3.01-3.780.0527.6286541100
3.78-29.2230.04432.628499199

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.76→29.223 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.797 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.091
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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. 1,2-ETHANEDIOL MOLECULES FROM THE CRYSTALLIZATION CONDITIONS HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.19 1398 5 %RANDOM
Rwork0.162 ---
obs0.163 27782 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.478 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20.3 Å20 Å2
2--0.59 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.76→29.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1604 0 12 204 1820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221728
X-RAY DIFFRACTIONr_bond_other_d0.0010.021133
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.9722360
X-RAY DIFFRACTIONr_angle_other_deg0.98432815
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9685242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.76925.71470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.68115301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.813155
X-RAY DIFFRACTIONr_chiral_restr0.0920.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021960
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02323
X-RAY DIFFRACTIONr_nbd_refined0.2130.2351
X-RAY DIFFRACTIONr_nbd_other0.1920.21195
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2847
X-RAY DIFFRACTIONr_nbtor_other0.0890.2857
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2165
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1580.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.218
X-RAY DIFFRACTIONr_mcbond_it1.86231185
X-RAY DIFFRACTIONr_mcbond_other0.4613456
X-RAY DIFFRACTIONr_mcangle_it2.50251790
X-RAY DIFFRACTIONr_scbond_it4.7858671
X-RAY DIFFRACTIONr_scangle_it6.04611556
LS refinement shellResolution: 1.76→1.81 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 109 -
Rwork0.218 1869 -
all-1978 -
obs--98.95 %
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)
11.1771-0.02020.35031.5381-0.7111.09730.03370.0231-0.0758-0.0640.11540.10040.0917-0.1528-0.1491-0.0127-0.0107-0.0453-0.04620.0377-0.0284-8.450665.313123.1685
21.26140.421-0.05491.2876-0.30081.46840.0464-0.1459-0.00330.2490.0081-0.0895-0.0980.003-0.05460.0152-0.0024-0.0538-0.05140.014-0.04792.661872.81832.5279
30.94340.05030.43711.0057-0.16680.86990.07010.1454-0.03530.0364-0.1076-0.21680.0920.15150.0375-0.02780.0201-0.0261-0.01580.01270.00511.130473.697318.9981
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 8820 - 107
2X-RAY DIFFRACTION2AA89 - 152108 - 171
3X-RAY DIFFRACTION3AA153 - 214172 - 233

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