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- PDB-4jg9: X-ray Crystal Structure of a Putative Lipoprotein from Bacillus a... -

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Basic information

Entry
Database: PDB / ID: 4jg9
TitleX-ray Crystal Structure of a Putative Lipoprotein from Bacillus anthracis
ComponentsLipoprotein
KeywordsLIPID BINDING PROTEIN / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyImmunoglobulin-like - #3830 / Protein of unknown function DUF4871 / Domain of unknown function (DUF4871) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta / Lipoprotein / Lipoprotein
Function and homology information
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.425 Å
AuthorsBrunzelle, J.S. / Wawrzak, Z. / Onopriyenko, O. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: X-ray Crystal Structure of a Putative Lipoprotein from Bacillus anthracis
Authors: Brunzelle, J.S. / Wawrzak, Z. / Onopriyenko, O. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases
History
DepositionFeb 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipoprotein
B: Lipoprotein


Theoretical massNumber of molelcules
Total (without water)39,5092
Polymers39,5092
Non-polymers00
Water1,56787
1
A: Lipoprotein

A: Lipoprotein


Theoretical massNumber of molelcules
Total (without water)39,5092
Polymers39,5092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+7/61
Buried area2030 Å2
ΔGint-6 kcal/mol
Surface area13310 Å2
MethodPISA
2
B: Lipoprotein

B: Lipoprotein


Theoretical massNumber of molelcules
Total (without water)39,5092
Polymers39,5092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+7/61
Buried area2110 Å2
ΔGint-6 kcal/mol
Surface area13130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.863, 85.863, 236.078
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Lipoprotein / Putative lipoprotein


Mass: 19754.713 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BA_0580, BAS0549, GBAA_0580 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q81VB7, UniProt: A0A6L7HR41*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.18 Å3/Da / Density % sol: 61.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.4M Na Citrate, 0.1M HEPES, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 29, 2012 / Details: Be Lens
RadiationMonochromator: Single Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.425→70.925 Å / Num. all: 20467 / Num. obs: 20467 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 13.3
Reflection shellResolution: 2.425→2.57 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3209 / % possible all: 100

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Processing

Software
NameVersionClassification
BLU-MAXdata collection
PHENIXAutoSolmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXAutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.425→70.925 Å / SU ML: 0.23 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.11 / Phase error: 20.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2096 1037 5.14 %RANDOM
Rwork0.1747 ---
obs0.1764 20384 99.89 %-
all-36880 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.425→70.925 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2214 0 0 87 2301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082272
X-RAY DIFFRACTIONf_angle_d1.1213108
X-RAY DIFFRACTIONf_dihedral_angle_d14.617834
X-RAY DIFFRACTIONf_chiral_restr0.073360
X-RAY DIFFRACTIONf_plane_restr0.005394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.425-2.48590.32761360.29822494X-RAY DIFFRACTION100
2.4859-2.55310.31561460.27942489X-RAY DIFFRACTION100
2.5531-2.62820.31341080.27062522X-RAY DIFFRACTION100
2.6282-2.7130.28561410.24792502X-RAY DIFFRACTION100
2.713-2.810.28511370.23492479X-RAY DIFFRACTION100
2.81-2.92250.29351530.22272489X-RAY DIFFRACTION100
2.9225-3.05550.2251550.20422490X-RAY DIFFRACTION100
3.0555-3.21660.19671570.19472483X-RAY DIFFRACTION100
3.2166-3.41820.19681230.16982507X-RAY DIFFRACTION100
3.4182-3.68210.20671400.16032496X-RAY DIFFRACTION100
3.6821-4.05260.16671190.15092523X-RAY DIFFRACTION100
4.0526-4.63890.17251320.12662492X-RAY DIFFRACTION100
4.6389-5.84410.17121290.1342512X-RAY DIFFRACTION100
5.8441-70.9250.20181180.17512508X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 26.7802 Å / Origin y: 41.4265 Å / Origin z: 128.9542 Å
111213212223313233
T0.4001 Å2-0.04 Å2-0.0072 Å2-0.3848 Å20.0288 Å2--0.2814 Å2
L1.6316 °2-0.6591 °2-0.5795 °2-1.1052 °20.7533 °2--1.5706 °2
S0.0116 Å °0.1974 Å °0.0923 Å °-0.1448 Å °-0.07 Å °-0.1041 Å °-0.1293 Å °0.0577 Å °0.0403 Å °
Refinement TLS groupSelection details: all

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