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- PDB-4elp: Ferric binding protein in apo form 2 -

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Basic information

Entry
Database: PDB / ID: 4elp
TitleFerric binding protein in apo form 2
ComponentsIron ABC transporter, periplasmic iron-binding protein
KeywordsMETAL TRANSPORT / beta sheet surrounded by alpha helices
Function / homology
Function and homology information


outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
Bacterial extracellular solute-binding protein / Ferric binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CARBONATE ION / Iron ABC transporter, periplasmic iron-binding protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsWang, Q. / Liu, X.Q. / Wang, X.Q.
CitationJournal: To be Published
Title: Crystal structure of ferric binding protein A
Authors: Wang, Q. / Liu, X.Q. / Wang, X.Q.
History
DepositionApr 11, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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

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Assembly

Deposited unit
A: Iron ABC transporter, periplasmic iron-binding protein
B: Iron ABC transporter, periplasmic iron-binding protein
C: Iron ABC transporter, periplasmic iron-binding protein
D: Iron ABC transporter, periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,3318
Polymers148,0914
Non-polymers2404
Water6,882382
1
A: Iron ABC transporter, periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0832
Polymers37,0231
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Iron ABC transporter, periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0832
Polymers37,0231
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Iron ABC transporter, periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0832
Polymers37,0231
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Iron ABC transporter, periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0832
Polymers37,0231
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.300, 139.227, 218.993
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Iron ABC transporter, periplasmic iron-binding protein / Ferric binding protein A


Mass: 37022.711 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHA1628 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SHV2
#2: Chemical
ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.18 Å3/Da / Density % sol: 43.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Li2SO4, 0.1M Bis-Tris, pH 6.5, 28% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. all: 80373 / Num. obs: 75069 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: dev_596)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→40.473 Å / FOM work R set: 0.8104 / SU ML: 0.3 / σ(F): 0 / Phase error: 25.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2598 3711 5.04 %random
Rwork0.1989 ---
all0.202 80373 --
obs0.202 73688 91.63 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.644 Å2 / ksol: 0.368 e/Å3
Displacement parametersBiso mean: 33.2446 Å2
Baniso -1Baniso -2Baniso -3
1-8.9239 Å2-0 Å2-0 Å2
2---3.0884 Å20 Å2
3----5.8355 Å2
Refinement stepCycle: LAST / Resolution: 2.07→40.473 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9552 0 16 382 9950
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079763
X-RAY DIFFRACTIONf_angle_d1.04213255
X-RAY DIFFRACTIONf_dihedral_angle_d14.3473647
X-RAY DIFFRACTIONf_chiral_restr0.0641504
X-RAY DIFFRACTIONf_plane_restr0.0051712
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0686-2.09480.33811130.23172181229478
2.0948-2.12240.29531100.21942362247284
2.1224-2.15150.27891390.19982357249687
2.1515-2.18220.28661290.2062369249886
2.1822-2.21480.31421400.20892348248884
2.2148-2.24940.30591170.21112375249286
2.2494-2.28630.30221410.21692402254387
2.2863-2.32570.32561040.21232444254886
2.3257-2.3680.28711260.21722399252586
2.368-2.41350.32641260.22172458258488
2.4135-2.46280.28691200.20852473259387
2.4628-2.51630.29871310.20482476260788
2.5163-2.57480.31391310.21312502263390
2.5748-2.63920.26381280.20572521264988
2.6392-2.71050.26951460.20572533267992
2.7105-2.79030.27551270.2062631275892
2.7903-2.88030.29381270.20982645277295
2.8803-2.98320.28571650.2242744290997
2.9832-3.10260.28821620.21192741290398
3.1026-3.24380.26821560.21252830298699
3.2438-3.41470.22241540.206227842938100
3.4147-3.62850.23841420.195928422984100
3.6285-3.90850.23671740.187428423016100
3.9085-4.30140.20871350.168228853020100
4.3014-4.92290.21121640.16252838300299
4.9229-6.19880.25451390.200229593098100
6.1988-40.4810.24431650.19473036320198
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)
10.1295-0.0553-0.03580.3723-0.07370.2557-0.13890.0421-0.0178-0.0440.31420.09260.0078-0.1590.09880.0616-0.0854-0.0180.10970.05690.142410.2241-16.2381-46.3973
20.09790.0152-0.04210.0359-0.00470.1861-0.09770.06320.10470.3150.17520.0698-0.2698-0.0461-0.0270.32570.07260.12390.08840.03150.142913.87218.3487-47.0293
30.05550.0103-0.0480.0675-0.01420.08170.0256-0.0086-0.04420.0087-0.0469-0.10340.03490.0173-0.021-0.1633-0.0745-0.08070.17510.04520.098130.7005-17.87628.0269
40.09970.0475-0.01320.1015-0.11380.3637-0.1076-0.01340.1601-0.054-0.06960.1293-0.38210.0667-0.16820.1913-0.09590.01220.07670.10670.032128.615216.08767.5855
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA23 - 330
2X-RAY DIFFRACTION2chain BB23 - 330
3X-RAY DIFFRACTION3chain CC23 - 330
4X-RAY DIFFRACTION4chain DD23 - 330

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