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- PDB-3gf6: Crystal structure of a bacterial lipoprotein (bt_1233) from bacte... -

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Basic information

Entry
Database: PDB / ID: 3gf6
TitleCrystal structure of a bacterial lipoprotein (bt_1233) from bacteroides thetaiotaomicron vpi-5482 at 1.69 A resolution
Componentsuncharacterized bacterial lipoprotein
KeywordsUNKNOWN FUNCTION / All-beta fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyProtein of unknown function DUF3845 / Protein of unknown function DUF3845 / Domain of Unknown Function with PDB structure / Jelly Rolls / Sandwich / Mainly Beta / Uncharacterized protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.69 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of bacterial lipoprotein of unknown function (NP_810146.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.69 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 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

Downloads & links

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Assembly

Deposited unit
A: uncharacterized bacterial lipoprotein
B: uncharacterized bacterial lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,29910
Polymers51,8022
Non-polymers4978
Water11,962664
1
A: uncharacterized bacterial lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2116
Polymers25,9011
Non-polymers3105
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: uncharacterized bacterial lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0874
Polymers25,9011
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.931, 75.541, 95.099
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A24 - 241
2115B24 - 241

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Components

#1: Protein uncharacterized bacterial lipoprotein


Mass: 25901.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_1233, NP_810146.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A8D4
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 664 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 22-244) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 22-244) 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: 2.18 Å3/Da / Density % sol: 43.62 %
Description: THE AND R MERGE VALUES REPORTED HERE ARE BASED ON TREATING FRIEDEL PAIRS AS SEPARATE REFLECTIONS.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 31.3000% polyethylene glycol 6000, 0.1M MES pH 6.5, NANODROP, 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: 0.97951
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 17, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.69→48.337 Å / Num. obs: 51502 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.776 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.69-1.750.6371.91832050641100
1.75-1.820.5072.41837650501100
1.82-1.90.3663.3180484962199.9
1.9-20.2494.8184705076199.9
2-2.130.2756.7265985306199.9
2.13-2.290.2518.8311444989199.9
2.29-2.520.21511.33775151751100
2.52-2.890.13815.73815752371100
2.89-3.630.06925.23745851691100
3.63-48.3370.04634.7378785473199.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.69→48.337 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.09 / SU B: 5.153 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.108
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 0.85 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. ETHYLENE GLYCOLS (EDO) USED AS CRYOPROTECTANT WERE MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.211 2615 5.1 %RANDOM
Rwork0.161 ---
obs0.163 51442 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 55.23 Å2 / Biso mean: 17.218 Å2 / Biso min: 2.31 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å20 Å20 Å2
2--1.68 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.69→48.337 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3495 0 32 664 4191
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223746
X-RAY DIFFRACTIONr_bond_other_d0.0010.022606
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.9795087
X-RAY DIFFRACTIONr_angle_other_deg0.83836368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0365485
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75124.624186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3515657
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1271521
X-RAY DIFFRACTIONr_chiral_restr0.0910.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214215
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02784
X-RAY DIFFRACTIONr_mcbond_it1.6532248
X-RAY DIFFRACTIONr_mcbond_other0.7033907
X-RAY DIFFRACTIONr_mcangle_it2.47153653
X-RAY DIFFRACTIONr_scbond_it3.75781498
X-RAY DIFFRACTIONr_scangle_it5.215111409
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A1258MEDIUM POSITIONAL0.190.5
A1543LOOSE POSITIONAL0.645
B1258MEDIUM THERMAL1.082
B1543LOOSE THERMAL1.310
LS refinement shellResolution: 1.69→1.734 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 214 -
Rwork0.27 3542 -
all-3756 -
obs--99.95 %
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)
10.69720.2691-0.03790.6342-0.28670.4149-0.03050.0989-0.0504-0.0450.0347-0.0056-0.0112-0.0454-0.00420.00670.00050.00130.0204-0.00730.00435.868553.256812.7702
20.6780.2458-0.10720.4106-0.0140.60290.03190.0348-0.1082-0.0407-0.0265-0.01820.0142-0.0869-0.00540.01180.001-0.00660.0338-0.0170.028463.515979.832921.432
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 242
2X-RAY DIFFRACTION2B24 - 241

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