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- PDB-5ev7: The crystal structure of a functionally unknown conserved protein... -

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Basic information

Entry
Database: PDB / ID: 5ev7
TitleThe crystal structure of a functionally unknown conserved protein mutant from Bacillus anthracis str. Ames
ComponentsConserved domain protein
KeywordsUNKNOWN FUNCTION / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


Peptidase M60, enhancin-like domain 3 / Peptidase M60, enhancin-like domain 1 / Immunoglobulin-like - #3600 / Peptidase M60, enhancin-like domain 2 / M60-like domain, N-terminal / N-terminal domain of M60-like peptidases / Peptidase family M60 domain / Peptidase M60, enhancin-like domain 3 / Peptidase M60, enhancin and enhancin-like / Peptidase family M60 domain profile. ...Peptidase M60, enhancin-like domain 3 / Peptidase M60, enhancin-like domain 1 / Immunoglobulin-like - #3600 / Peptidase M60, enhancin-like domain 2 / M60-like domain, N-terminal / N-terminal domain of M60-like peptidases / Peptidase family M60 domain / Peptidase M60, enhancin-like domain 3 / Peptidase M60, enhancin and enhancin-like / Peptidase family M60 domain profile. / Peptidase M60-like family / Neutral Protease; domain 2 / Collagenase (Catalytic Domain) / Jelly Rolls / Immunoglobulin-like / Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Conserved domain protein / Conserved domain protein
Similarity search - Component
Biological speciesBacillus anthracis str. Ames (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.351 Å
AuthorsTan, K. / Zhou, M. / Jedrzejczak, R. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
CitationJournal: To Be Published
Title: The crystal structure of a functionally unknown conserved protein mutant from Bacillus anthracis str. Ames.
Authors: Tan, K. / Zhou, M. / Jedrzejczak, R. / Anderson, W.F. / Joachimiak, A.
History
DepositionNov 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conserved domain protein


Theoretical massNumber of molelcules
Total (without water)60,1631
Polymers60,1631
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.157, 155.567, 49.152
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Conserved domain protein


Mass: 60163.199 Da / Num. of mol.: 1 / Mutation: E299D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis str. Ames (bacteria)
Gene: BA_5305 / Plasmid: pMCSG7 / Cell line (production host): BL21(DE3)magic / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0J9WYN5, UniProt: A0A0F7RB18*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 47.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 24% (w/v) PEG1500, 20% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.35→37 Å / Num. all: 24158 / Num. obs: 24158 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 42.2 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 23.4
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FCA

4fca


Resolution: 2.351→36.578 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1157 4.8 %Random selectio
Rwork0.2177 ---
obs0.2194 24110 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.351→36.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3791 0 0 19 3810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023888
X-RAY DIFFRACTIONf_angle_d0.6195279
X-RAY DIFFRACTIONf_dihedral_angle_d12.3741413
X-RAY DIFFRACTIONf_chiral_restr0.025558
X-RAY DIFFRACTIONf_plane_restr0.003692
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3508-2.45780.34641330.32362839X-RAY DIFFRACTION100
2.4578-2.58730.34681240.30572820X-RAY DIFFRACTION100
2.5873-2.74940.32281450.30122823X-RAY DIFFRACTION100
2.7494-2.96160.36151350.29442829X-RAY DIFFRACTION100
2.9616-3.25950.28171460.28022858X-RAY DIFFRACTION100
3.2595-3.73070.25531580.22882846X-RAY DIFFRACTION100
3.7307-4.69870.22151530.17322898X-RAY DIFFRACTION100
4.6987-36.58290.19251630.15243040X-RAY DIFFRACTION100
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)
13.49993.086-2.7084.4906-3.00544.2798-0.313-0.1593-0.6339-0.3593-0.4747-0.94320.33060.55890.30020.1720.01880.09880.44620.07590.4395-7.584224.91941.3684
22.1420.5854-0.80390.4222-0.77491.02241.30710.43551.96242.0578-0.21091.9967-1.56750.0489-0.44261.0278-0.01590.76110.3253-0.15261.0604-31.008230.631818.0972
34.50090.5776-1.57114.187-1.86972.76530.8524-0.43660.40091.1107-0.39840.6032-0.63670.2026-0.08490.581-0.17990.2630.4217-0.10510.4512-32.036616.332326.0384
46.06080.4543-0.88065.7484-2.09833.90750.28830.5037-1.9127-0.5202-0.5441-0.61120.06380.69860.44890.32290.05150.04390.5336-0.02460.7207-18.3618-1.866815.0218
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 44 through 276 )
2X-RAY DIFFRACTION2chain 'A' and (resid 277 through 359 )
3X-RAY DIFFRACTION3chain 'A' and (resid 360 through 458 )
4X-RAY DIFFRACTION4chain 'A' and (resid 459 through 525 )

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