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- PDB-4ghb: Crystal structure of a porin-like protein (BACUNI_01323) from Bac... -

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Basic information

Entry
Database: PDB / ID: 4ghb
TitleCrystal structure of a porin-like protein (BACUNI_01323) from Bacteroides uniformis ATCC 8492 at 2.32 A resolution
Componentshypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / a porin like fold / uncharacterized protein of PF06788 family / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


Porin - #190 / Domain of unknown function DUF4595 with porin-like fold / Domain of unknown function (DUF4595) with porin-like fold / OmpA-like domain / OmpA-like domain profile. / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
OmpA-like domain-containing protein
Similarity search - Component
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.32 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BACUNI_01323) from Bacteroides uniformis ATCC 8492 at 2.32 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 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 ...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: hypothetical protein
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,31825
Polymers61,2902
Non-polymers2,02923
Water7,837435
1
A: hypothetical protein
B: hypothetical protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)379,910150
Polymers367,73812
Non-polymers12,172138
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area69550 Å2
ΔGint-901 kcal/mol
Surface area118670 Å2
MethodPISA
2
A: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,88915
Polymers30,6451
Non-polymers1,24514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,42910
Polymers30,6451
Non-polymers7849
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)168.615, 168.615, 147.749
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein hypothetical protein


Mass: 30644.803 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis (bacteria) / Strain: ATCC 8492 / Gene: BACUNI_01323 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7V185
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (42-312) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (42-312) 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: 4.95 Å3/Da / Density % sol: 75.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2.4M ammonium sulfate, 0.1M TRIS pH 8.0, 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: 0.97916,0.91837,0.97849
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2012
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979161
20.918371
30.978491
ReflectionResolution: 2.32→44.215 Å / Num. obs: 53889 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 55.956 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 17.81
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.32-2.40.852.449554509299.8
2.4-2.50.7043.153577552099.7
2.5-2.610.5484.247117512599.7
2.61-2.750.3186.455282540299.9
2.75-2.920.2021053118525999.8
2.92-3.150.13614.954380546399.9
3.15-3.460.08922.448302523899.8
3.46-3.960.06132.6542795435100
3.96-4.980.04838.449224547399.9
4.980.04240.553625579599.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEMarch 15, 2012data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.32→44.215 Å / Cor.coef. Fo:Fc: 0.9532 / Cor.coef. Fo:Fc free: 0.9474 / Occupancy max: 1 / Occupancy min: 0.5 / 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. CL, SO4 AND GOL MODELED ARE PRESENT IN CRYSTALLIZATION CONDITIONS. 5. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 6. THE DIFFERENCE MAP IN THE SOLVENT REGION IS NOISY, LIKELY DUE TO HIGH SOLVENT CONTENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.1945 2737 5.08 %RANDOM
Rwork0.1744 ---
obs0.1754 53849 99.82 %-
Displacement parametersBiso max: 167.28 Å2 / Biso mean: 55.254 Å2 / Biso min: 29.42 Å2
Baniso -1Baniso -2Baniso -3
1--3.7121 Å20 Å20 Å2
2---3.7121 Å20 Å2
3---7.4241 Å2
Refine analyzeLuzzati coordinate error obs: 0.276 Å
Refinement stepCycle: LAST / Resolution: 2.32→44.215 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4017 0 122 435 4574
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1939SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes111HARMONIC2
X-RAY DIFFRACTIONt_gen_planes627HARMONIC5
X-RAY DIFFRACTIONt_it4299HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion624SEMIHARMONIC5
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_contact4851SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4299HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5873HARMONIC21.12
X-RAY DIFFRACTIONt_omega_torsion3.9
X-RAY DIFFRACTIONt_other_torsion2.76
LS refinement shellResolution: 2.32→2.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2577 206 5.3 %
Rwork0.2153 3679 -
all0.2175 3885 -
obs--99.82 %
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)
11.241-0.18760.12832.2420.16011.15730.08910.0757-0.3005-0.0799-0.06120.14560.1853-0.1401-0.028-0.05180.0243-0.0598-0.1365-0.0274-0.038753.625825.177916.4771
20.85830.23580.18810.93780.09670.96090.01160.07160.0118-0.005-0.0107-0.03370.01030.1442-0.0009-0.08480.0658-0.03960.03430.0405-0.056955.140259.798414.9571
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|55 - 312}A55 - 312
2X-RAY DIFFRACTION2{B|53 - 312}B53 - 312

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