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- PDB-4ipb: Crystal structure of a DUF2874 family protein (BACOVA_02504) from... -

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Basic information

Entry
Database: PDB / ID: 4ipb
TitleCrystal structure of a DUF2874 family protein (BACOVA_02504) from Bacteroides ovatus ATCC 8483 at 1.62 A resolution
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF11396 family protein / DUF2874 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyNuclear Transport Factor 2; Chain: A, - #360 / Putative beta-lactamase-inhibitor-like, PepSY-like / Putative beta-lactamase-inhibitor-like, PepSY-like / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / DI(HYDROXYETHYL)ETHER / PepSY_like domain-containing protein
Function and homology information
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.62 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BACOVA_02504) from Bacteroides ovatus ATCC 8483 at 1.62 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 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
Revision 1.5Oct 30, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,8204
Polymers32,6212
Non-polymers1982
Water6,215345
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5093
Polymers16,3111
Non-polymers1982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)16,3111
Polymers16,3111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.265, 54.155, 60.120
Angle α, β, γ (deg.)90.000, 91.420, 90.000
Int Tables number4
Space group name H-MP1211
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Uncharacterized protein


Mass: 16310.724 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Strain: ATCC 8483 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7LXE2
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 22-162 OF 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: 2.06 Å3/Da / Density % sol: 40.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 12.0% polyethylene glycol 20000, 0.1M MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.918401, 0.979415, 0.979261
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2012 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9184011
20.9794151
30.9792611
ReflectionResolution: 1.62→29.044 Å / Num. all: 33727 / Num. obs: 33727 / % possible obs: 99.7 % / Redundancy: 3.6 % / Rsym value: 0.1 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.62-1.6630.7680.9713123970.76896.7
1.66-1.713.60.6231.1870824280.623100
1.71-1.763.60.4961.4863923700.496100
1.76-1.813.70.4071.7832222740.407100
1.81-1.873.70.3052.3823122420.30599.9
1.87-1.943.60.223785421520.22100
1.94-2.013.60.1783.8750920590.178100
2.01-2.093.70.1444.6729019900.144100
2.09-2.183.70.1275.4706719330.12799.9
2.18-2.293.60.1086.2666918300.10899.9
2.29-2.413.60.1026.4633817430.10299.8
2.41-2.563.60.0946.9590116310.094100
2.56-2.743.60.0896.6567215850.089100
2.74-2.963.60.0817.3519314490.081100
2.96-3.243.60.0757.8476813350.07599.8
3.24-3.623.50.0689425112060.06899.8
3.62-4.183.40.0629.5361010720.062100
4.18-5.123.40.0598.830629120.05999.8
5.12-7.243.70.0658.526457160.065100
7.24-29.0443.50.0754.514214030.07598.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.20data scaling
REFMACrefinement
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.62→29.044 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 0.23 / SU B: 3.712 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.096
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. A PEG FRAGMENT (PEG) AND A GLYCEROL (GOL) MOLECULE FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2027 1708 5.1 %RANDOM
Rwork0.1655 ---
obs0.1674 33695 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 78.05 Å2 / Biso mean: 23.1169 Å2 / Biso min: 7.84 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å2-0 Å20.42 Å2
2--1.55 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.62→29.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2243 0 13 345 2601
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022358
X-RAY DIFFRACTIONr_bond_other_d0.0060.022193
X-RAY DIFFRACTIONr_angle_refined_deg1.6491.9473228
X-RAY DIFFRACTIONr_angle_other_deg1.16135037
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6675293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.56225.093108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.12715332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.455156
X-RAY DIFFRACTIONr_chiral_restr0.1070.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212709
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02573
X-RAY DIFFRACTIONr_mcbond_it1.941.4591140
X-RAY DIFFRACTIONr_mcbond_other1.9281.4531139
X-RAY DIFFRACTIONr_mcangle_it2.8842.7031425
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 132 -
Rwork0.308 2240 -
all-2372 -
obs--95.92 %
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)
11.440.21850.63380.35240.1732.19010.0251-0.0779-0.1058-0.0080.0433-0.06470.15260.1166-0.06840.14560.0283-0.00610.042-0.00360.10828.5962.76429.756
21.7472-0.3377-1.25130.6620.14472.83730.00820.00830.02910.05390.0171-0.0855-0.03610.1706-0.02520.1469-0.012-0.03030.0526-0.00810.088810.07911.6350.039
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 161
2X-RAY DIFFRACTION2B0 - 161

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