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- PDB-4elo: Ferric binding protein in apo form 1 -

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Basic information

Entry
Database: PDB / ID: 4elo
TitleFerric binding protein in apo form 1
ComponentsIron ABC transporter, periplasmic iron-binding protein
KeywordsMETAL TRANSPORT / beta sheet surrounded by alpha helices
Function / homologyBacterial extracellular solute-binding protein / Ferric binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / outer membrane-bounded periplasmic space / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / Iron ABC transporter, periplasmic iron-binding protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.914 Å
AuthorsWang, Q. / Liu, X.Q. / Wang, X.Q.
CitationJournal: To be Published
Title: Crystal structure of the 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
E: Iron ABC transporter, periplasmic iron-binding protein
F: Iron ABC transporter, periplasmic iron-binding protein


Theoretical massNumber of molelcules
Total (without water)222,1366
Polymers222,1366
Non-polymers00
Water29,4181633
1
A: Iron ABC transporter, periplasmic iron-binding protein


Theoretical massNumber of molelcules
Total (without water)37,0231
Polymers37,0231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Iron ABC transporter, periplasmic iron-binding protein


Theoretical massNumber of molelcules
Total (without water)37,0231
Polymers37,0231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Iron ABC transporter, periplasmic iron-binding protein


Theoretical massNumber of molelcules
Total (without water)37,0231
Polymers37,0231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Iron ABC transporter, periplasmic iron-binding protein


Theoretical massNumber of molelcules
Total (without water)37,0231
Polymers37,0231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Iron ABC transporter, periplasmic iron-binding protein


Theoretical massNumber of molelcules
Total (without water)37,0231
Polymers37,0231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Iron ABC transporter, periplasmic iron-binding protein


Theoretical massNumber of molelcules
Total (without water)37,0231
Polymers37,0231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.124, 139.349, 326.337
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.: 6
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1633 / 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: 2.16 Å3/Da / Density % sol: 42.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M ammonium acetate, 30% PEG 4000, 0.1M Sodium acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 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: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. all: 149713 / Num. obs: 143194 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 20.4 Å2

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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: SAD / Resolution: 1.914→36.148 Å / FOM work R set: 0.871 / SU ML: 0.21 / σ(F): 0 / Phase error: 19.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2073 7123 5.02 %random
Rwork0.1634 ---
all0.1656 149713 --
obs0.1656 141958 94.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.874 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso mean: 24.7725 Å2
Baniso -1Baniso -2Baniso -3
1-3.7278 Å2-0 Å2-0 Å2
2---2.9633 Å20 Å2
3----0.7645 Å2
Refinement stepCycle: LAST / Resolution: 1.914→36.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14328 0 0 1633 15961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714637
X-RAY DIFFRACTIONf_angle_d1.03119879
X-RAY DIFFRACTIONf_dihedral_angle_d12.7285479
X-RAY DIFFRACTIONf_chiral_restr0.0662257
X-RAY DIFFRACTIONf_plane_restr0.0052564
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9144-1.93620.27331690.19793512368176
1.9362-1.9590.25992600.18764095435589
1.959-1.98290.25521970.17624247444490
1.9829-2.0080.24112160.17134169438588
2.008-2.03440.23052180.15674173439191
2.0344-2.06230.2082090.15224250445991
2.0623-2.09170.21422370.154354459192
2.0917-2.12290.20972270.15434233446090
2.1229-2.15610.23492410.16364251449293
2.1561-2.19140.24452420.16534392463493
2.1914-2.22920.23562100.15654413462392
2.2292-2.26980.18622350.15594358459394
2.2698-2.31340.22992480.15494468471695
2.3134-2.36060.2252500.15684476472695
2.3606-2.41190.2292340.1634466470096
2.4119-2.4680.21212490.16354594484396
2.468-2.52970.22292170.17024508472596
2.5297-2.59810.21952730.1654563483697
2.5981-2.67450.19212480.16374635488398
2.6745-2.76080.22842730.16364614488799
2.7608-2.85950.2292410.17054703494499
2.8595-2.97390.22422330.1764725495899
2.9739-3.10920.22592450.17994684492999
3.1092-3.2730.22152620.17954767502999
3.273-3.47790.22892420.16954763500599
3.4779-3.74620.18532360.15964760499699
3.7462-4.12270.18682530.156448125065100
4.1227-4.71820.16152540.135548575111100
4.7182-5.94010.15272460.153349155161100
5.9401-36.15440.19332580.18065078533698
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)
10.32290.07610.33120.57010.23440.7106-0.0302-0.0631-0.0265-0.06670.00240.0139-0.0421-0.0104-0.0444-0.00680.00560.01130.0896-0.00090.082222.182153.424546.0202
20.4697-0.2632-0.13890.4857-0.26720.8995-0.05380.01870.0280.0826-0.0046-0.0471-0.1002-0.0538-0.00480.069-0.0195-0.01360.08210.01750.064441.494117.606961.8232
30.45750.0021-0.32250.1350.02390.6455-0.04690.02060.02450.04910.02230.00610.0358-0.0295-0.00960.0143-0.014-0.01540.04560.02130.06222.038518.07937.8879
40.1946-0.11470.42530.6604-0.4281.3093-0.02690.0175-0.0021-0.0759-0.0332-0.03060.1720.0769-0.110.0999-0.0140.00640.07980.00440.069323.6778-16.18867.2781
50.33830.2637-0.36680.877-0.42280.93530.0199-0.03340.037-0.0414-0.02310.0232-0.16990.0203-0.03650.09990.01240.00230.0538-0.01920.07417.722987.928346.7138
60.43910.12370.43830.7440.1680.80170.0310.0249-0.0450.0933-0.036-0.06480.15070.0453-0.11060.1104-0.0113-0.00770.07970.00650.090341.5467-16.598363.0228
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
5X-RAY DIFFRACTION5chain EE23 - 330
6X-RAY DIFFRACTION6chain FF23 - 330

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