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- PDB-3sz6: IsdX1, an anthrax hemophore -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 3sz6
TitleIsdX1, an anthrax hemophore
ComponentsConserved domain protein
KeywordsHEME-BINDING PROTEIN / Ig fold / hemophore
Function / homology
Function and homology information


extracellular region / metal ion binding
Similarity search - Function
Immunoglobulin-like - #1850 / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / : / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Iron Transport-associated domain protein / Iron Transport-associated domain protein
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsPoor, C.B. / Maresso, A.W. / Murphy, F. / He, C.
CitationJournal: Plos Pathog. / Year: 2012
Title: Differential function of lip residues in the mechanism and biology of an anthrax hemophore.
Authors: Ekworomadu, M.T. / Poor, C.B. / Owens, C.P. / Balderas, M.A. / Fabian, M. / Olson, J.S. / Murphy, F. / Balkabasi, E. / Honsa, E.S. / He, C. / Goulding, C.W. / Maresso, A.W.
History
DepositionJul 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Conserved domain protein
B: Conserved domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7225
Polymers27,5592
Non-polymers1633
Water2,900161
1
A: Conserved domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8152
Polymers13,7801
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Conserved domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9073
Polymers13,7801
Non-polymers1282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.637, 43.659, 47.408
Angle α, β, γ (deg.)99.24, 96.53, 107.35
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Conserved domain protein / Iron Transport-associated domain protein


Mass: 13779.596 Da / Num. of mol.: 2 / Fragment: UNP residues 26-146
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: BAS4443, BA_4788, GBAA_4788 / Production host: Escherichia coli (E. coli) / References: UniProt: Q81L44, UniProt: A0A6L8PY92*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.55 Å3/Da / Density % sol: 51.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 2 M NaCl, 0.1 M citric acid (pH 3.5) , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 18, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.8→46.1 Å / Num. all: 25248 / Num. obs: 24541 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.8→1.86 Å / % possible all: 94.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→25.574 Å / SU ML: 0.24 / σ(F): 0.06 / Phase error: 26.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2342 2314 10.12 %random
Rwork0.2087 ---
obs0.2113 22863 90.47 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.859 Å2 / ksol: 0.464 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.3499 Å21.8666 Å2-3.0107 Å2
2--1.2253 Å2-6.4771 Å2
3----7.5752 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1880 0 8 161 2049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021951
X-RAY DIFFRACTIONf_angle_d0.5662632
X-RAY DIFFRACTIONf_dihedral_angle_d8.939747
X-RAY DIFFRACTIONf_chiral_restr0.038295
X-RAY DIFFRACTIONf_plane_restr0.002333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8004-1.83720.3512960.2845894X-RAY DIFFRACTION65
1.8372-1.87710.3767960.2857921X-RAY DIFFRACTION70
1.8771-1.92080.31761140.24151033X-RAY DIFFRACTION76
1.9208-1.96880.28951440.20921113X-RAY DIFFRACTION85
1.9688-2.0220.25841440.21121169X-RAY DIFFRACTION90
2.022-2.08150.24621350.20311256X-RAY DIFFRACTION94
2.0815-2.14860.26871320.20351270X-RAY DIFFRACTION94
2.1486-2.22540.23271450.20521259X-RAY DIFFRACTION96
2.2254-2.31440.25731460.19791259X-RAY DIFFRACTION94
2.3144-2.41970.25291370.22231272X-RAY DIFFRACTION95
2.4197-2.54710.25541520.21881252X-RAY DIFFRACTION95
2.5471-2.70660.26381390.23491294X-RAY DIFFRACTION96
2.7066-2.91530.26241420.23751302X-RAY DIFFRACTION97
2.9153-3.20810.22441430.21471291X-RAY DIFFRACTION98
3.2081-3.67120.21311540.19951340X-RAY DIFFRACTION99
3.6712-4.62090.18211490.16831315X-RAY DIFFRACTION99
4.6209-25.57680.22491460.21791309X-RAY DIFFRACTION98
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)
11.9096-0.4783-1.00331.0411-0.0751.84530.03740.2103-0.0491-0.1561-0.09010.0094-0.0119-0.22550.05530.14760.01950.00350.1991-0.00360.12646.40016.46542.0083
21.7070.44131.63290.9070.21992.4926-0.0489-0.25730.06830.2351-0.0740.08030.1949-0.36730.10730.22460.01520.00840.2031-0.01180.164-6.446918.3866-17.0553
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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