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- PDB-6all: Crystal structure of a predicted ferric/iron (III) hydroxymate si... -

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Basic information

Entry
Database: PDB / ID: 6all
TitleCrystal structure of a predicted ferric/iron (III) hydroxymate siderophore substrate binding protein from Bacillus anthracis
ComponentsFe(3+)-citrate-binding protein yfmC
KeywordsMETAL TRANSPORT / structural genomics / NIAID / national institute of allergy and infectious diseases / PERIPLASMIC LIGAND BINDING PROTEIN / SUBSTRATE BINDING PROTEIN / ABC TRANSPORT PROTEIN / alpha/beta protein / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


: / ATPase-coupled transmembrane transporter activity / iron ion transport / iron ion binding / plasma membrane
Similarity search - Function
ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PE3 / Petrobactin-binding protein FpuA
Similarity search - Component
Biological speciesBacillus anthracis str. 'Ames Ancestor' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsStogios, P.J. / Wawrzak, Z. / Skarina, T. / Grimshaw, S. / Savchenko, A. / Anderson, W.F. / 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: Crystal structure of a predicted ferric/iron (III) hydroxymate siderophore substrate binding protein from Bacillus anthracis
Authors: Stogios, P.J.
History
DepositionAug 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: Fe(3+)-citrate-binding protein yfmC
B: Fe(3+)-citrate-binding protein yfmC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1555
Polymers72,2512
Non-polymers1,9043
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-16 kcal/mol
Surface area24720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.505, 125.505, 60.262
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-510-

HOH

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Components

#1: Protein Fe(3+)-citrate-binding protein yfmC / Iron compound ABC transporter / iron compound-binding protein


Mass: 36125.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis str. 'Ames Ancestor' (bacteria)
Gene: yfmC, GBAA_4766, BASH2_01198 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q81L65
#2: Chemical ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL / Polyethylene glycol


Mass: 634.751 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C28H58O15
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 1.9 Å3/Da / Density % sol: 35.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 0.2 MgCl2, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.47→30 Å / Num. obs: 19698 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.023 / Net I/σ(I): 41.07
Reflection shellResolution: 2.47→2.51 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.929 / Mean I/σ(I) obs: 2.07 / Num. unique obs: 980 / CC1/2: 0.745 / Rpim(I) all: 0.378 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_2733refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EFD

1efd


Resolution: 2.47→29.036 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 36.21
RfactorNum. reflection% reflectionSelection details
Rfree0.2903 980 4.98 %RANDOM
Rwork0.2375 ---
obs0.24 19677 99.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.47→29.036 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4481 0 33 49 4563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064583
X-RAY DIFFRACTIONf_angle_d0.9026169
X-RAY DIFFRACTIONf_dihedral_angle_d22.2881741
X-RAY DIFFRACTIONf_chiral_restr0.05706
X-RAY DIFFRACTIONf_plane_restr0.004787
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4658-2.59570.43661380.3752627X-RAY DIFFRACTION98
2.5957-2.75820.41400.34222644X-RAY DIFFRACTION100
2.7582-2.9710.3761370.31542672X-RAY DIFFRACTION100
2.971-3.26960.35771440.30092649X-RAY DIFFRACTION100
3.2696-3.74180.31461400.25342681X-RAY DIFFRACTION100
3.7418-4.71110.2561400.20792685X-RAY DIFFRACTION100
4.7111-29.03790.24381410.19732739X-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)
12.86110.1918-0.69723.9248-1.52384.82320.5241-0.70130.60510.6404-0.3736-0.0333-0.64920.8369-0.18240.5388-0.29940.04430.7298-0.07360.983843.868443.657943.8654
21.74340.6302-1.90518.1025-1.15337.54520.15490.3810.1612-0.2449-0.35570.3560.0931-0.27270.15520.3030.0541-0.04930.58340.07510.677436.826231.936422.2646
37.65764.13765.17552.98084.23339.0746-2.32740.3464-1.1504-0.01050.1459-1.1928-0.79321.12721.60941.7477-0.01060.01991.89820.43061.530454.295426.436521.851
44.81470.21520.9519.7813-3.35881.87830.36520.377-0.5998-2.6576-0.589-0.77441.88830.48950.4831.11930.37310.46970.91490.29040.856543.997126.915911.5925
58.0771.6134-0.74975.0501-1.97512.19150.2880.05320.7717-0.307-0.478-0.363-0.65371.48470.17890.6173-0.11890.07880.6930.15511.125944.643343.209424.5648
66.06760.28831.22097.49884.22696.14190.21180.33420.1164-0.8971-0.1181-0.86780.1408-0.0833-0.09661.08120.15450.11890.55180.06630.610439.20741.076718.5715
77.2064-0.3938-0.46836.54731.73077.2750.38890.465-0.0495-0.5838-0.60350.97420.9266-0.55320.12581.1647-0.0555-0.09210.5713-0.04110.470628.30551.51221.1857
85.97422.75810.60678.17850.23536.6579-0.2813-0.6930.11990.7057-0.20220.64711.6854-0.16780.31470.95530.10650.13280.60220.01410.423832.84416.419844.8932
96.29722.57944.01386.01162.39676.4251-0.0529-0.34940.63260.3969-0.73120.09150.4708-0.19040.830.79220.0884-0.05420.5164-0.03770.517634.677914.614142.8518
103.0985-0.6566-1.35694.5965-1.41655.86270.0975-0.45920.03031.249-0.5284-0.56262.22330.86160.39861.1940.1582-0.07260.64780.06810.515538.51327.618447.9594
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 37:191)
2X-RAY DIFFRACTION2(chain A and resid 192:266)
3X-RAY DIFFRACTION3(chain A and resid 267:274)
4X-RAY DIFFRACTION4(chain A and resid 275:296)
5X-RAY DIFFRACTION5(chain A and resid 297:322)
6X-RAY DIFFRACTION6(chain B and resid 36:128)
7X-RAY DIFFRACTION7(chain B and resid 129:176)
8X-RAY DIFFRACTION8(chain B and resid 177:215)
9X-RAY DIFFRACTION9(chain B and resid 216:276)
10X-RAY DIFFRACTION10(chain B and resid 277:324)

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