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- PDB-4ifa: 1.5 Angstrom resolution crystal structure of an extracellular pro... -

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Basic information

Entry
Database: PDB / ID: 4ifa
Title1.5 Angstrom resolution crystal structure of an extracellular protein containing a SCP domain from Bacillus anthracis str. Ames
ComponentsExtracellular protein containing a SCP domain
KeywordsUNKNOWN FUNCTION / extracellular protein containing a SCP domain / vaccine candidate / virulence / pathogenesis / Center for Structural Genomics of Infectious Diseases / CSGID / NIAID / National Institute of Allergy and Infectious Diseases / alpha/beta fold
Function / homology
Function and homology information


CAP-associated domain / CAP-associated N-terminal / Pathogenesis-related Protein p14a / CAP / CAP domain / Cysteine-rich secretory protein family / CAP superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsHalavaty, A.S. / Minasov, G. / Dubrovska, I. / Winsor, J. / Shuvalova, L. / Shatsman, S. / Peterson, S.N. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.5 Angstrom resolution crystal structure of an extracellular protein containing a SCP domain from Bacillus anthracis str. Ames
Authors: Halavaty, A.S. / Minasov, G. / Dubrovska, I. / Winsor, J. / Shuvalova, L. / Shatsman, S. / Peterson, S.N. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Oct 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 / 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: Extracellular protein containing a SCP domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,87510
Polymers39,2151
Non-polymers6609
Water8,827490
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.115, 86.118, 89.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Extracellular protein containing a SCP domain


Mass: 39214.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BA_4147, BAS3849, GBAA_4147 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/Magic / References: UniProt: Q81W36, UniProt: A0A348A8R7*PLUS

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Non-polymers , 5 types, 499 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 490 / 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: 2.25 Å3/Da / Density % sol: 45.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: protein at 7.7 mg/mL in 10 mM Tris-HCL pH 8.3 500 mM NaCl, 5 mM BME, crystallization: The Classics II Suite (condition G11: 200 mM Mg Cl2, 100 mM Bis-Tris pH 6.5, 25% (w/v) PEG3350 , VAPOR ...Details: protein at 7.7 mg/mL in 10 mM Tris-HCL pH 8.3 500 mM NaCl, 5 mM BME, crystallization: The Classics II Suite (condition G11: 200 mM Mg Cl2, 100 mM Bis-Tris pH 6.5, 25% (w/v) PEG3350 , 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: Dec 10, 2012 / Details: Be Lenses
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 56956 / Num. obs: 56956 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 47
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2809 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
HKL-3000phasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.5→29.67 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.459 / SU ML: 0.042 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18304 2908 5.1 %RANDOM
Rwork0.15353 ---
obs0.15504 54572 99.89 %-
all-54572 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.292 Å2
Baniso -1Baniso -2Baniso -3
1-1.99 Å2-0 Å2-0 Å2
2---1.37 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2416 0 38 490 2944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222679
X-RAY DIFFRACTIONr_bond_other_d0.0010.021820
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.953646
X-RAY DIFFRACTIONr_angle_other_deg0.91234449
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2865334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.08125.315143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.315462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3021513
X-RAY DIFFRACTIONr_chiral_restr0.1040.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213090
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02537
X-RAY DIFFRACTIONr_mcbond_it0.9211.51600
X-RAY DIFFRACTIONr_mcbond_other0.3071.5644
X-RAY DIFFRACTIONr_mcangle_it1.522603
X-RAY DIFFRACTIONr_scbond_it2.36631079
X-RAY DIFFRACTIONr_scangle_it3.6384.51043
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 229 -
Rwork0.194 3983 -
obs-3983 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)
13.38110.15281.33412.15970.64414.4744-0.0980.40730.5283-0.6075-0.02020.0005-0.9232-0.02340.11810.3839-0.0095-0.01590.15530.07660.18567.22462.200348.4705
21.4066-0.06030.44971.4039-0.40451.7186-0.0116-0.14670.04660.02560.10340.24180.0585-0.2284-0.09190.0051-0.0120.00550.09930.03160.12880.75440.87927.4346
32.98870.14592.12493.68760.22037.2140.28940.1225-0.4263-0.6823-0.24180.62650.9444-0.3403-0.04760.41670.0334-0.12480.1478-0.08130.33947.4358-17.244416.7175
43.2198-0.08590.66132.4727-0.45692.33770.11620.2888-0.2995-0.4572-0.0190.15960.4220.0698-0.09720.14180.027-0.04030.0611-0.00390.10359.703-7.760218.2387
53.3970.21051.81951.3567-0.34463.9057-0.01570.11840.0542-0.20430.10630.2529-0.0775-0.2462-0.09060.0385-0.0073-0.03610.07930.03510.11731.998910.918912.9994
60.90170.20320.00171.894-0.18792.4456-0.03330.00550.0577-0.23780.0212-0.0245-0.28910.15040.01210.0735-0.033-0.00060.0454-0.00140.052115.968615.236611.4269
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A41 - 51
2X-RAY DIFFRACTION2A52 - 131
3X-RAY DIFFRACTION3A132 - 153
4X-RAY DIFFRACTION4A154 - 205
5X-RAY DIFFRACTION5A212 - 236
6X-RAY DIFFRACTION6A237 - 344

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