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- PDB-3g6i: Crystal structure of an outer membrane protein, part of a putativ... -

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Basic information

Entry
Database: PDB / ID: 3g6i
TitleCrystal structure of an outer membrane protein, part of a putative carbohydrate binding complex (bt_1022) from bacteroides thetaiotaomicron vpi-5482 at 1.93 A resolution
ComponentsPutative outer membrane protein, part of carbohydrate binding complex
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyProtein of unknown function DUF3826 / Protein of unknown function (DUF3826) / DI(HYDROXYETHYL)ETHER / Uncharacterized protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.93 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of outer membrane protein, part of carbohydrate binding complex (NP_809935.1) from Bacteroides thetaiotaomicron VPI-5482 at 1.93 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_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

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Assembly

Deposited unit
A: Putative outer membrane protein, part of carbohydrate binding complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5464
Polymers23,2381
Non-polymers3083
Water4,288238
1
A: Putative outer membrane protein, part of carbohydrate binding complex
hetero molecules

A: Putative outer membrane protein, part of carbohydrate binding complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0928
Polymers46,4762
Non-polymers6176
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area2000 Å2
ΔGint-18.1 kcal/mol
Surface area22290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.025, 75.025, 127.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Putative outer membrane protein, part of carbohydrate binding complex


Mass: 23237.840 Da / Num. of mol.: 1 / Fragment: UNP residues 20-222
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Strain: VPI-5482 / DSM 2079 / NCTC 10582 / E50 / Gene: BT_1022, NP_809935.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A8Z5
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 20-222) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 20-222) 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: 3.85 Å3/Da / Density % sol: 68.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.67
Details: NANODROP, 0.25M Lithium sulfate, 34.0% PEG 4000, 0.1M Tris-HCl pH 8.67, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837, 0.97964, 0.97949
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 17, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979641
30.979491
ReflectionResolution: 1.93→48.97 Å / Num. obs: 28120 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Biso Wilson estimate: 34.847 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 14.99
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.93-21.5561.51978627661100
2-2.080.9832.51976727411100
2.08-2.170.59741906226371100
2.17-2.290.4185.62097029041100
2.29-2.430.4597.92570727141100
2.43-2.620.48611.24052028091100
2.62-2.880.29615.93979327851100
2.88-3.30.14723.53998228521100
3.3-4.150.07534.43894628561100
4.15-48.970.0539.5401653073199.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.93→48.97 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 5.967 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.118
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 RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. SULFATE AND PEG FRAGMENTS MODELED ARE PRESENT IN CRYSTALLIZATION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1409 5 %RANDOM
Rwork0.197 ---
obs0.198 28048 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.24 Å2 / Biso mean: 32.801 Å2 / Biso min: 11.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2--0.67 Å20 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 1.93→48.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1585 0 19 238 1842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221713
X-RAY DIFFRACTIONr_bond_other_d0.0020.021192
X-RAY DIFFRACTIONr_angle_refined_deg1.371.9692317
X-RAY DIFFRACTIONr_angle_other_deg0.91732929
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6275225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24525.29485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.60915328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.811510
X-RAY DIFFRACTIONr_chiral_restr0.0850.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021921
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02335
X-RAY DIFFRACTIONr_mcbond_it1.73231039
X-RAY DIFFRACTIONr_mcbond_other0.5253422
X-RAY DIFFRACTIONr_mcangle_it2.89151673
X-RAY DIFFRACTIONr_scbond_it5.1498674
X-RAY DIFFRACTIONr_scangle_it7.63411632
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 89 -
Rwork0.371 1926 -
all-2015 -
obs--99.85 %
Refinement TLS params.Method: refined / Origin x: 32.5962 Å / Origin y: 16.237 Å / Origin z: 68.2445 Å
111213212223313233
T0.0268 Å2-0.0013 Å20.0008 Å2-0.0329 Å20.007 Å2--0.0091 Å2
L0.6209 °2-0.0918 °20.4542 °2-0.6469 °2-0.0659 °2--0.6914 °2
S0.0068 Å °-0.0381 Å °-0.0489 Å °-0.0413 Å °0.0162 Å °-0.0355 Å °0.0792 Å °0.0102 Å °-0.0229 Å °

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