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- PDB-4hde: The crystal structure of a SCO1/SenC family lipoprotein from Baci... -

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Basic information

Entry
Database: PDB / ID: 4hde
TitleThe crystal structure of a SCO1/SenC family lipoprotein from Bacillus anthracis str. Ames
ComponentsSCO1/SenC family lipoprotein
KeywordsLIPID BINDING PROTEIN / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID / NIAID / National Institute of Allergy and Infectious Diseases
Function / homology
Function and homology information


Copper chaperone SCO1/SenC / SCO1/SenC / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SCO1/SenC family lipoprotein / SCO1/SenC family lipoprotein
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.317 Å
AuthorsTan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: The crystal structure of a SCO1/SenC family lipoprotein from Bacillus anthracis str. Ames
Authors: Tan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionOct 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 9, 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 / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SCO1/SenC family lipoprotein


Theoretical massNumber of molelcules
Total (without water)19,8291
Polymers19,8291
Non-polymers00
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.985, 48.468, 88.551
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS EXPERIMENTALLY UNKNOWN. It is predicted to be a monomer.

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Components

#1: Protein SCO1/SenC family lipoprotein


Mass: 19828.539 Da / Num. of mol.: 1 / Fragment: UNP residues 29-195
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BAS2093, BA_2249, GBAA_2249 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q81R11, UniProt: A0A6L7H5L6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 1.89 Å3/Da / Density % sol: 35.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.05M Magnessium chloride, 0.1M HEPES:NaOH, 30%(w/v)PEG MME550, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 12, 2012 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 1.317→23 Å / Num. all: 35792 / Num. obs: 35792 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 33.9
Reflection shellResolution: 1.317→1.34 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1795 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.317→22.56 Å / SU ML: 0.29 / σ(F): 1.35 / Phase error: 18.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.185 1791 5.01 %random
Rwork0.1617 ---
obs0.1629 35718 98.08 %-
all-35718 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.775 Å2 / ksol: 0.334 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.5197 Å2-0 Å20 Å2
2---2.9094 Å2-0 Å2
3---0.3897 Å2
Refinement stepCycle: LAST / Resolution: 1.317→22.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1359 0 0 249 1608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061423
X-RAY DIFFRACTIONf_angle_d1.0421930
X-RAY DIFFRACTIONf_dihedral_angle_d11.799548
X-RAY DIFFRACTIONf_chiral_restr0.075211
X-RAY DIFFRACTIONf_plane_restr0.006250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3172-1.35280.27041310.25122423X-RAY DIFFRACTION93
1.3528-1.39260.22761490.2282618X-RAY DIFFRACTION100
1.3926-1.43760.22691250.20962575X-RAY DIFFRACTION100
1.4376-1.48890.23461320.1922647X-RAY DIFFRACTION100
1.4889-1.54850.20461150.17552641X-RAY DIFFRACTION100
1.5485-1.6190.19461230.16632649X-RAY DIFFRACTION99
1.619-1.70430.19391390.1592619X-RAY DIFFRACTION100
1.7043-1.81110.18241490.15752630X-RAY DIFFRACTION99
1.8111-1.95080.1961580.16332596X-RAY DIFFRACTION99
1.9508-2.1470.18781280.16262627X-RAY DIFFRACTION99
2.147-2.45730.19131390.16252629X-RAY DIFFRACTION98
2.4573-3.09470.20681590.16482596X-RAY DIFFRACTION97
3.0947-22.56340.14671440.14272677X-RAY DIFFRACTION94
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)
13.64421.9794-1.15312.2887-0.77121.8292-0.0626-0.0016-0.0957-0.02740.02660.00560.0157-0.05450.05280.0620.0210.00170.0728-0.00580.066926.887925.358-18.8147
21.12270.06390.4252.3491-0.09991.7921-0.0341-0.02910.04480.1710.0056-0.0218-0.04150.00950.02290.0877-0.00160.01410.12940.00160.105733.612124.9109-8.0228
31.13320.0805-0.05091.76230.1860.7884-0.00110.02210.12520.03550.00510.0396-0.1157-0.02290.00230.1204-0.00160.00190.12160.00170.0830.45634.8519-10.9488
42.44960.42521.51122.09060.49565.2730.0333-0.0714-0.1040.0524-0.0126-0.07330.1504-0.0924-0.00670.1153-0.01540.02360.13330.00850.136525.478116.0233-7.6433
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 28:55)
2X-RAY DIFFRACTION2chain 'A' and (resseq 56:100)
3X-RAY DIFFRACTION3chain 'A' and (resseq 101:165)
4X-RAY DIFFRACTION4chain 'A' and (resseq 166:195)

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