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- PDB-4les: 2.2 Angstrom Crystal Structure of Conserved Hypothetical Protein ... -

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Basic information

Entry
Database: PDB / ID: 4les
Title2.2 Angstrom Crystal Structure of Conserved Hypothetical Protein from Bacillus anthracis.
ComponentsProtein - conserved hypothetical
KeywordsUNKNOWN FUNCTION / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / Conserved Hypothetical / Unknown
Function / homology
Function and homology information


Immunoglobulin-like - #1240 / Immunoprotective extracellular, immunoglobulin-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ETHANOL / TRIETHYLENE GLYCOL / PHOSPHATE ION / DUF4352 domain-containing protein / DUF4352 domain-containing protein
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsMinasov, G. / Wawrzak, Z. / Filippova, E. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Grimshaw, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.2 Angstrom Crystal Structure of Conserved Hypothetical Protein from Bacillus anthracis.
Authors: Minasov, G. / Wawrzak, Z. / Filippova, E. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Grimshaw, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJun 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Oct 30, 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 / 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: Protein - conserved hypothetical
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1346
Polymers23,7611
Non-polymers3735
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.754, 95.754, 41.518
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Protein - conserved hypothetical


Mass: 23760.992 Da / Num. of mol.: 1 / Fragment: UNP residues 28-209
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BA_0915, BAS0864, GBAA_0915 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q81UG1, UniProt: A0A6L8PRR7*PLUS

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Non-polymers , 5 types, 44 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.31 Å3/Da / Density % sol: 46.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: Protein: 7.4 mG/mL, 0.25 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3; Screen: JSCG+ (C6), 0.1 M Phosphate-citrate buffer pH 4.2, 40% (v/v) PEG 300, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 17, 2013 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 11282 / Num. obs: 11282 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 51 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 32.2
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 3.5 / Num. unique all: 552 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
REFMAC5.8.0046refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→29.34 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 10.778 / SU ML: 0.128
Isotropic thermal model: Thermal Factors Individually Isotropically Refined
Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21151 538 4.8 %RANDOM
Rwork0.17529 ---
all0.17693 10690 --
obs0.17693 10690 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.726 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0.03 Å2-0 Å2
2---0.07 Å2-0 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1151 0 22 39 1212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191223
X-RAY DIFFRACTIONr_bond_other_d0.0010.021182
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.9711645
X-RAY DIFFRACTIONr_angle_other_deg0.69632747
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2755148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.02126.20758
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.97415227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.307153
X-RAY DIFFRACTIONr_chiral_restr0.0940.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021362
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02253
X-RAY DIFFRACTIONr_mcbond_it2.2563.017586
X-RAY DIFFRACTIONr_mcbond_other2.2573.017585
X-RAY DIFFRACTIONr_mcangle_it3.2894.506736
X-RAY DIFFRACTIONr_mcangle_other3.2874.506737
X-RAY DIFFRACTIONr_scbond_it3.6623.595637
X-RAY DIFFRACTIONr_scbond_other3.6573.595637
X-RAY DIFFRACTIONr_scangle_other5.8295.16910
X-RAY DIFFRACTIONr_long_range_B_refined9.69525.4131313
X-RAY DIFFRACTIONr_long_range_B_other9.67125.1431304
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 38 -
Rwork0.188 778 -
obs-778 100 %
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)
11.80890.44850.24125.08945.513413.02030.2245-0.1191-0.00830.02410.1568-0.32670.16810.0238-0.38130.15450.13740.01440.22330.01870.084927.016938.812116.8008
23.0924-2.27150.74134.42290.25616.6078-0.0076-0.4810.15810.37520.1866-0.30780.42440.1336-0.1790.19060.15420.0110.36740.0280.196234.637434.933223.4705
35.14855.61452.060714.23572.88026.21790.16830.16350.1492-0.81090.1508-0.35930.27790.6733-0.31910.21410.1610.10530.280.04360.147536.726936.06488.4807
412.26585.2591-12.469915.0682-8.440420.0906-0.5334-0.1113-0.88580.022-0.0459-0.58751.89870.71280.57930.39980.23330.0150.2523-0.01420.241937.67730.060523.5293
53.9708-8.20082.087817.1413-4.37321.1176-0.29060.08680.04910.74150.1282-0.35-0.1598-0.020.16250.69410.1338-0.0580.4431-0.15780.488231.341420.930311.6454
65.8818-1.29491.55217.65212.54825.88840.1848-0.12850.01360.1670.1875-1.5989-0.05310.7154-0.37230.08350.05950.03760.3019-0.01070.20538.517441.229420.7656
74.0475-1.1570.02317.5983.80868.7990.15640.160.7141-0.61870.0927-0.5607-1.18760.3554-0.24910.29420.07660.11820.23620.06290.305932.661446.99612.7093
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A68 - 91
2X-RAY DIFFRACTION2A92 - 128
3X-RAY DIFFRACTION3A129 - 148
4X-RAY DIFFRACTION4A149 - 165
5X-RAY DIFFRACTION5A166 - 179
6X-RAY DIFFRACTION6A180 - 189
7X-RAY DIFFRACTION7A190 - 209

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