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- PDB-3o0l: Crystal structure of a Pfam DUF1425 family member (Shew_1734) fro... -

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Basic information

Entry
Database: PDB / ID: 3o0l
TitleCrystal structure of a Pfam DUF1425 family member (Shew_1734) from Shewanella sp. pv-4 at 1.81 a resolution
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PFAM DUF1425 FAMILY MEMBER / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homologyImmunoglobulin-like - #3230 / Protein of unknown function DUF1425 / YcfL-like superfamily / Protein of unknown function (DUF1425) / Immunoglobulin-like / Sandwich / Mainly Beta / Uncharacterized protein
Function and homology information
Biological speciesShewanella loihica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.81 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Pfam DUF1425 family member (Shew_1734) from Shewanella SP. PV-4 at 1.81 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8315
Polymers24,6452
Non-polymers1863
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-14 kcal/mol
Surface area11820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.633, 62.633, 119.040
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Uncharacterized protein


Mass: 12322.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella loihica (bacteria) / Strain: ATCC BAA-1088 / PV-4 / Gene: Shew_1734 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A3QDQ3
#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.: 157 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 26-335) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 26-335) 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: 2.73 Å3/Da / Density % sol: 55.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.14
Details: 1.4100M ammonium sulfate, 0.2000M sodium chloride, 0.1M sodium acetate pH 4.14, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97920,0.97860
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 11, 2010 / 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
10.918371
20.97921
30.97861
ReflectionResolution: 1.81→29.76 Å / Num. all: 25352 / Num. obs: 25352 / % possible obs: 99.9 % / Redundancy: 6 % / Biso Wilson estimate: 31.397 Å2 / Rsym value: 0.065 / Net I/σ(I): 13.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.81-1.866.10.742.21119018350.74100
1.86-1.916.10.75511105218110.755100
1.91-1.9660.4211.71059617540.421100
1.96-2.026.10.322.41036317000.32100
2.02-2.096.10.25331006916560.253100
2.09-2.166.10.1873.9977515960.187100
2.16-2.2560.1883.7934415450.188100
2.25-2.3460.1723.4889814850.172100
2.34-2.446.10.1146.2876714350.114100
2.44-2.566.10.0937.3827113550.093100
2.56-2.76.10.0847.8798113140.084100
2.7-2.866.10.0778.2763312600.077100
2.86-3.0660.0718.7693411500.071100
3.06-3.360.05810.7671711110.058100
3.3-3.6260.0511.7602710050.05100
3.62-4.0560.04314.255549250.043100
4.05-4.675.80.04413.148238250.044100
4.67-5.725.80.04513.141397160.04599.9
5.72-8.095.50.04414.130945600.044100
8.09-29.764.70.0471414883140.04791.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
REFMAC5.5.0110refinement
SCALA3.3.15data scaling
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.81→29.76 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 6.01 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.12 / Phase error: 31.397
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 RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. ETHYLENE GLYCOL (EDO) MODELED IS PRESENT IN CRYSTALLIZATION/CRYO BUFFER.
RfactorNum. reflection% reflectionSelection details
Rfree0.2275 1276 5.1 %RANDOM
Rwork0.2041 ---
obs0.2052 25123 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.75 Å2 / Biso mean: 38.988 Å2 / Biso min: 18.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20.47 Å20 Å2
2--0.95 Å20 Å2
3----1.42 Å2
Refinement stepCycle: LAST / Resolution: 1.81→29.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1655 0 12 157 1824
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221822
X-RAY DIFFRACTIONr_bond_other_d0.0020.021239
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.9442492
X-RAY DIFFRACTIONr_angle_other_deg0.89633049
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5475256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.37623.84678
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6215331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5921514
X-RAY DIFFRACTIONr_chiral_restr0.1020.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022067
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02371
X-RAY DIFFRACTIONr_mcbond_it2.12331136
X-RAY DIFFRACTIONr_mcbond_other0.5853468
X-RAY DIFFRACTIONr_mcangle_it3.61251858
X-RAY DIFFRACTIONr_scbond_it5.4668686
X-RAY DIFFRACTIONr_scangle_it7.85311612
LS refinement shellResolution: 1.81→1.857 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 85 -
Rwork0.303 1745 -
all-1830 -
obs--100 %
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)
10.550.2692-0.73160.3230.37153.8082-0.04740.1202-0.1213-0.03530.0232-0.0995-0.0175-0.28220.02420.06920.04950.03320.12320.02660.06126.098220.64950.1545
23.3911-1.1353-0.17111.5337-0.34460.9557-0.12120.11360.22540.1399-0.0175-0.1047-0.11750.15050.13880.0297-0.0402-0.01330.0933-0.00110.06336.590330.4381-14.5103
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 128
2X-RAY DIFFRACTION2B22 - 129

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