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- PDB-4qoa: Crystal structure of a putative periplasmic protein (BACUNI_04550... -

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Basic information

Entry
Database: PDB / ID: 4qoa
TitleCrystal structure of a putative periplasmic protein (BACUNI_04550) from Bacteroides uniformis ATCC 8492 at 2.75 A resolution
ComponentsPutative periplasmic protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Two copies of DUF2874 domain (PF11396) / BLIP-like fold / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyInhibitor of vertebrate lysozyme, Ivy - #30 / Putative beta-lactamase-inhibitor-like, PepSY-like / Putative beta-lactamase-inhibitor-like, PepSY-like / Inhibitor of vertebrate lysozyme, Ivy / 3-Layer(aba) Sandwich / Alpha Beta / Putative beta-lactamase-inhibitor-like PepSY-like domain-containing protein
Function and homology information
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.75 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative periplasmic protein (BACUNI_04550) from Bacteroides uniformis ATCC 8492 at 2.75 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Feb 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 1.3Oct 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

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Assembly

Deposited unit
A: Putative periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7943
Polymers14,6701
Non-polymers1242
Water30617
1
A: Putative periplasmic protein
hetero molecules

A: Putative periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5886
Polymers29,3392
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+2/31
Buried area4410 Å2
ΔGint-24 kcal/mol
Surface area15110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.311, 103.311, 90.830
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Putative periplasmic protein


Mass: 14669.667 Da / Num. of mol.: 1 / Fragment: UNP residues 21-146
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis (bacteria) / Gene: BACUNI_04550 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7VAB9
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING GLY 0 FOLLOWED BY RESIDUES 21-146 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: 4.77 Å3/Da / Density % sol: 74.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 24.00% polyethylene glycol 3350, 0.16M tri-ammonium citrate, 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: 0.9116,0.9794,0.9793
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2014
Details: Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91161
20.97941
30.97931
ReflectionResolution: 2.75→29.823 Å / Num. all: 7860 / Num. obs: 7860 / % possible obs: 99.8 % / Redundancy: 9.1 % / Rsym value: 0.084 / Net I/σ(I): 15.7
Reflection shell

Rmerge(I) obs: 0.012 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.75-2.828.80.750005651.185100
2.82-2.98.10.743935431.054100
2.9-2.989.91.253255370.66799.9
2.98-3.07101.451855200.541100
3.07-3.189.61.748355030.453100
3.18-3.299.32.946154970.261100
3.29-3.4193.542084660.21399.9
3.41-3.557.94.736914670.15699.7
3.55-3.719.56.441754410.116100
3.71-3.899.77.341054230.1100
3.89-4.19.58.839044110.07899.8
4.1-4.359.11034923820.061100
4.35-4.658.311.630053640.051100
4.65-5.029.212.731353400.05100
5.02-5.59.511.330583220.056100
5.5-6.159.21026882910.06499.7
6.15-7.17.511.419622630.05699.9
7.1-8.79.114.920942310.04100
8.7-12.38.316.614871790.03499.4
12.3-29.8236.917.77961150.03393.1

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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
BUSTER-TNT2.10.0refinement
MOSFLMdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.75→29.823 Å / Cor.coef. Fo:Fc: 0.9249 / Cor.coef. Fo:Fc free: 0.9142 / Occupancy max: 1 / Occupancy min: 0.75 / 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 THE REFINEMENT. 4. 1,2-ETHANEDIOL USED AS A CRYOPROTECTANT WAS MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2498 361 4.6 %RANDOM
Rwork0.215 ---
obs0.2166 7840 99.83 %-
Displacement parametersBiso max: 158.89 Å2 / Biso mean: 87.8228 Å2 / Biso min: 50.71 Å2
Baniso -1Baniso -2Baniso -3
1-14.8621 Å20 Å20 Å2
2--14.8621 Å20 Å2
3----29.7241 Å2
Refine analyzeLuzzati coordinate error obs: 0.535 Å
Refinement stepCycle: LAST / Resolution: 2.75→29.823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1005 0 8 17 1030
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d487SINUSOIDAL6
X-RAY DIFFRACTIONt_trig_c_planes30HARMONIC2
X-RAY DIFFRACTIONt_gen_planes142HARMONIC5
X-RAY DIFFRACTIONt_it1030HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion140SEMIHARMONIC5
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_contact1105SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1030HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg1389HARMONIC21.17
X-RAY DIFFRACTIONt_omega_torsion2.49
X-RAY DIFFRACTIONt_other_torsion2.27
LS refinement shellResolution: 2.75→3.07 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2982 101 4.67 %
Rwork0.2617 2061 -
all0.2635 2162 -
obs--99.83 %
Refinement TLS params.Method: refined / Origin x: 28.7089 Å / Origin y: 24.7284 Å / Origin z: 28.5723 Å
111213212223313233
T-0.1368 Å20.0861 Å20.0272 Å2--0.1862 Å20.0637 Å2--0.0583 Å2
L1.8469 °2-1.3048 °2-1.6263 °2-2.0029 °21.5563 °2--2.2761 °2
S-0.1975 Å °-0.024 Å °0.1807 Å °0.2042 Å °-0.0189 Å °-0.3548 Å °0.4577 Å °-0.2557 Å °0.2164 Å °

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