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- PDB-4elq: Ferric binding protein with carbonate -

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Basic information

Entry
Database: PDB / ID: 4elq
TitleFerric binding protein with carbonate
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: 1.893 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1654
Polymers74,0452
Non-polymers1202
Water7,368409
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
MethodPISA
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
MethodPISA
Unit cell
Length a, b, c (Å)66.489, 61.663, 73.940
Angle α, β, γ (deg.)90.00, 111.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 37022.711 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: CO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 35.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M MaCl, 0.1M Bis-Tris pH 5.5, 25% 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: 1.893→40 Å / Num. all: 44314 / Num. obs: 44182 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 19.23 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: MOLECULAR REPLACEMENT / Resolution: 1.893→36.256 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8354 / SU ML: 0.24 / σ(F): 0 / Phase error: 23.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 2134 5.03 %random
Rwork0.1718 ---
all0.1745 44314 --
obs0.1745 42398 95.44 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.875 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso max: 95.66 Å2 / Biso mean: 25.386 Å2 / Biso min: 5.55 Å2
Baniso -1Baniso -2Baniso -3
1-2.8185 Å2-0 Å26.1897 Å2
2--1.6715 Å20 Å2
3----4.4899 Å2
Refinement stepCycle: LAST / Resolution: 1.893→36.256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4802 0 8 409 5219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064910
X-RAY DIFFRACTIONf_angle_d1.0416668
X-RAY DIFFRACTIONf_dihedral_angle_d13.1731836
X-RAY DIFFRACTIONf_chiral_restr0.065756
X-RAY DIFFRACTIONf_plane_restr0.005862
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8932-1.93720.3281090.22552213232279
1.9372-1.98560.29371440.19792472261690
1.9856-2.03930.27111200.18022585270592
2.0393-2.09930.23211230.17512663278694
2.0993-2.16710.25211510.18022637278895
2.1671-2.24450.27211250.17542689281496
2.2445-2.33440.24621320.17222705283796
2.3344-2.44060.25121530.1762705285897
2.4406-2.56920.241670.17772733290097
2.5692-2.73020.24541370.17972740287798
2.7302-2.94090.24591430.18672780292398
2.9409-3.23670.23451750.18642776295199
3.2367-3.70460.18341600.165428322992100
3.7046-4.66590.19911330.145628372970100
4.6659-36.26260.18381620.160828973059100
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)
10.4391-0.1353-0.35660.34530.07620.4364-0.00150.1295-0.04510.0075-0.0397-0.00530.0291-0.14550.01090.0443-0.0149-0.01570.08160.00450.06532.0265-9.704532.6167
20.3021-0.077-0.23130.17750.29740.5313-0.0244-0.05690.00370.03220.0051-0.03460.12360.038-0.02740.1066-0.0069-0.00190.08020.01450.0776.42884.841663.1871
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA21 - 330
2X-RAY DIFFRACTION2chain BB21 - 330

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