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- PDB-4gbs: Crystal structure of a putative lipoprotein (BF2707) from Bactero... -

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Basic information

Entry
Database: PDB / ID: 4gbs
TitleCrystal structure of a putative lipoprotein (BF2707) from Bacteroides fragilis NCTC 9343 at 2.75 A resolution
ComponentsPutative lipoprotein
KeywordsLIPID BINDING PROTEIN / PF14064 family / transport / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / HEME-BINDING PROTEIN
Function / homologyHmuY protein / HmuY protein / Putative lipoprotein
Function and homology information
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.48 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative lipoprotein (BF2707) from Bacteroides fragilis NCTC 9343 at 2.75 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative lipoprotein
B: Putative lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4134
Polymers46,2212
Non-polymers1922
Water1,29772
1
A: Putative lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2072
Polymers23,1111
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2072
Polymers23,1111
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.009, 66.009, 263.457
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Putative lipoprotein /


Mass: 23110.564 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: NCTC 9343 / Gene: BF2707, BF9343_2622 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LBW5
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Sequence details1. THE CONSTRUCT (RESIDUES 25-223) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG ...1. THE CONSTRUCT (RESIDUES 25-223) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. 2. THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO CRYSTALLIZATION.

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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: 3.1 Å3/Da / Density % sol: 60.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 2.40M ammonium sulfate, 0.1M Bicine pH 9.0, 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: 0.9795,0.9184
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 31, 2012
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
10.97951
20.91841
ReflectionResolution: 2.48→46.676 Å / Num. obs: 21701 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 76.09 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.078 / Net I/σ(I): 14.65 / Num. measured all: 137544
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.48-2.570.7051.171.714273213821331.26999.8
2.57-2.670.7850.7752.413410207620650.84399.5
2.67-2.790.870.5633.212508208920790.61799.5
2.79-2.940.9540.2975.713972217821760.32499.9
2.94-3.120.9860.189.314282210221010.195100
3.12-3.360.9950.10514.414460216221570.11499.8
3.36-3.70.9980.06720.614086217821760.07299.9
3.7-4.230.9980.0524.812596218621740.05599.5
4.23-5.310.9990.04430.814381222222150.04899.7
5.31-46.6760.9980.053013576248324410.05598.3

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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: 2.48→46.676 Å / Cor.coef. Fo:Fc: 0.9462 / Cor.coef. Fo:Fc free: 0.9335 / 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. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS).5.THE PROTEIN WAS SUBJECTED TO REDUCTIVE METHYLATION PRIOR TO CRYSTALLIZATION. LYSINE 101 APPEARS TO HAVE BEEN PROTECTED FROM REDUCTIVE METHYLATION AND WAS MODELED AS LYSINE. ALL OTHER LYSINES HAVE BEEN MODELED AS N-DIMETHYL-LYSINE (MLY). 6. SULFATE MOLECULES(SO4) FROM THE CRYSTALLIZATION HAVE BEEN MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 1106 5.11 %RANDOM
Rwork0.1969 ---
obs0.1983 21634 99.67 %-
Displacement parametersBiso max: 180.26 Å2 / Biso mean: 76.5292 Å2 / Biso min: 37.51 Å2
Baniso -1Baniso -2Baniso -3
1--2.5059 Å20 Å20 Å2
2---2.5059 Å20 Å2
3---5.0117 Å2
Refine analyzeLuzzati coordinate error obs: 0.467 Å
Refinement stepCycle: LAST / Resolution: 2.48→46.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2933 0 10 72 3015
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1322SINUSOIDAL8
X-RAY DIFFRACTIONt_trig_c_planes78HARMONIC2
X-RAY DIFFRACTIONt_gen_planes431HARMONIC5
X-RAY DIFFRACTIONt_it3027HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion407SEMIHARMONIC5
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_contact3419SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3027HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg4143HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion3.58
X-RAY DIFFRACTIONt_other_torsion2.13
LS refinement shellResolution: 2.48→2.6 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2816 151 5.41 %
Rwork0.23 2641 -
all0.2326 2792 -
obs--99.67 %
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)
16.75550.09262.18414.10181.183.66960.0772-0.48430.61490.0732-0.3397-0.15510.222-0.44310.2625-0.3116-0.1059-0.0358-0.0265-0.089-0.132473.418299.428726.4875
24.4258-2.4755-3.50165.01443.49446.57740.26670.4238-0.2718-0.6655-0.30920.3241-0.1569-0.1330.0425-0.18450.0047-0.1575-0.0805-0.0466-0.2406111.40894.36410.2489
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|35 - 223 }A35 - 223
2X-RAY DIFFRACTION2{ B|38 - 223 }B38 - 223

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