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- PDB-4fmr: Crystal structure of a Putative bacterial DNA binding protein (BV... -

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Basic information

Entry
Database: PDB / ID: 4fmr
TitleCrystal structure of a Putative bacterial DNA binding protein (BVU_2165) from Bacteroides vulgatus ATCC 8482 at 2.25 A resolution
Componentsuncharacterized hypothetical protein
KeywordsStructural Genomics / Unknown Function / Bacterial DNA binding protein / DUF4469 with IG-like fold / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


Domain of unknown function DUF4469 with IG-like fold / : / Domain of unknown function (DUF4469) with IG-like fold / DNA-binding domain / HU Protein; Chain A / IHF-like DNA-binding proteins / Coagulation Factor XIII; Chain A, domain 1 - #70 / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Few Secondary Structures ...Domain of unknown function DUF4469 with IG-like fold / : / Domain of unknown function (DUF4469) with IG-like fold / DNA-binding domain / HU Protein; Chain A / IHF-like DNA-binding proteins / Coagulation Factor XIII; Chain A, domain 1 - #70 / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Few Secondary Structures / Irregular / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesBacteroides vulgatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BVU_2165) from Bacteroides vulgatus ATCC 8482 at 2.25 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
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 / struct_ref_seq_dif
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
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

Downloads & links

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Assembly

Deposited unit
A: uncharacterized hypothetical protein
B: uncharacterized hypothetical protein
C: uncharacterized hypothetical protein
D: uncharacterized hypothetical protein


Theoretical massNumber of molelcules
Total (without water)113,8084
Polymers113,8084
Non-polymers00
Water10,251569
1
A: uncharacterized hypothetical protein
B: uncharacterized hypothetical protein


Theoretical massNumber of molelcules
Total (without water)56,9042
Polymers56,9042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8410 Å2
ΔGint-59 kcal/mol
Surface area20900 Å2
MethodPISA
2
C: uncharacterized hypothetical protein
D: uncharacterized hypothetical protein


Theoretical massNumber of molelcules
Total (without water)56,9042
Polymers56,9042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8470 Å2
ΔGint-61 kcal/mol
Surface area21070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.536, 143.307, 67.561
Angle α, β, γ (deg.)90.000, 94.350, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
uncharacterized hypothetical protein


Mass: 28452.002 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus (bacteria) / Strain: ATCC 8482 / Gene: BVU_2165 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A6L2B2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 569 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 2-265) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 2-265) 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: 2.53 Å3/Da / Density % sol: 51.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 20.0% 1,3-butanediol, 0.1M sodium acetate pH 4.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9794
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2012
Details: Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.25→29.682 Å / Num. obs: 52331 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 48.088 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 11.05
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.25-2.330.8891.432721995094.7
2.33-2.420.5572.5367321004498.5
2.42-2.530.4253.2378361039598.4
2.53-2.670.3144.3389271100198.5
2.67-2.830.2215.932930968095.4
2.83-3.050.1449385011050398.5
3.05-3.360.08513.9383711054598.2
3.36-3.840.06217.1351861008697.1
3.84-4.830.04225.2386591052999
4.830.03827.3367821031196.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 29, 2011data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: SAD / Resolution: 2.25→29.682 Å / Cor.coef. Fo:Fc: 0.9555 / Cor.coef. Fo:Fc free: 0.9311 / Occupancy max: 1 / Occupancy min: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. 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 ...Details: 1. 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. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5. THE REFINEMENT WAS RESTRAINED AGAINST THE MAD PHASES. 6. THE REGION CONTAINING AN RAMACHRANDRAN OUTLIER (C221) HAS POOR DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2656 5.08 %RANDOM
Rwork0.1689 ---
obs0.1711 52298 97.91 %-
Displacement parametersBiso max: 142.86 Å2 / Biso mean: 50.0499 Å2 / Biso min: 25.05 Å2
Baniso -1Baniso -2Baniso -3
1-1.6031 Å20 Å20.5626 Å2
2--0.777 Å20 Å2
3----2.3801 Å2
Refine analyzeLuzzati coordinate error obs: 0.282 Å
Refinement stepCycle: LAST / Resolution: 2.25→29.682 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7049 0 0 569 7618
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3483SINUSOIDAL4
X-RAY DIFFRACTIONt_trig_c_planes178HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1102HARMONIC5
X-RAY DIFFRACTIONt_it7298HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1035SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8730SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7298HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9926HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion3.66
X-RAY DIFFRACTIONt_other_torsion2.3
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2995 192 5.22 %
Rwork0.2432 3488 -
all0.2461 3680 -
obs--97.91 %
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)
10.64150.24470.05031.20710.14931.1936-0.008-0.02390.1120.08360.0282-0.0285-0.10870.1472-0.0202-0.10210.00610.0114-0.0515-0.0183-0.069613.3338-14.843618.9588
21.5883-0.35770.04391.4123-0.12790.4409-0.0186-0.2418-0.21790.15170.04960.06440.0554-0.0017-0.031-0.10920.00240.0128-0.04920.0074-0.09087.5797-37.749721.0918
30.421-0.1208-0.12461.29060.38552.4894-0.03060.008-0.0762-0.01920.0617-0.07080.37690.3574-0.0311-0.10980.0423-0.0078-0.07960.0027-0.113618.4908-5.009552.8729
40.82190.3747-0.30181.8997-0.57970.66760.00240.09770.1148-0.03080.05250.0286-0.0646-0.024-0.0548-0.10260.0071-0.0071-0.04260.0116-0.080514.134318.712450.9448
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|3 - 243 }A3 - 243
2X-RAY DIFFRACTION2{ B|0 - 244 }B0 - 244
3X-RAY DIFFRACTION3{ C|2 - 243 }C2 - 243
4X-RAY DIFFRACTION4{ D|0 - 243 }D0 - 243

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