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- PDB-7f6r: Crystal structure of metal-citrate-binding mutant (S164A) protein... -

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Basic information

Entry
Database: PDB / ID: 7f6r
TitleCrystal structure of metal-citrate-binding mutant (S164A) protein (MctA) of ABC transporter in apo state
ComponentsIron ABC transporter, periplasmic iron-binding protein
KeywordsTRANSPORT PROTEIN / Substrate-binding protein / metal ion / secondary transporter / symporter
Function / homologyBacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / CARBONATE ION / SULFITE ION / Iron ABC transporter, periplasmic iron-binding protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.09 Å
AuthorsKanaujia, S.P. / Mandal, S.K.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR16065/NER/95/61/2015 India
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Structural and thermodynamic insights into a novel Mg 2+ -citrate-binding protein from the ABC transporter superfamily.
Authors: Mandal, S.K. / Kanaujia, S.P.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2021
Title: Structural and thermodynamic insights into a novel Mg2+-citrate-binding protein from the ABC transporter superfamily
Authors: Mandal, S.K. / Kanaujia, S.P.
History
DepositionJun 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,13613
Polymers38,1671
Non-polymers96912
Water3,945219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-4 kcal/mol
Surface area13860 Å2
Unit cell
Length a, b, c (Å)44.530, 108.070, 163.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-542-

HOH

21A-629-

HOH

31A-712-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 38167.410 Da / Num. of mol.: 1 / Mutation: S164A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8) (bacteria)
Strain: ATCC 27634 / DSM 579 / HB8 / Gene: TTHB177 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q53VZ2

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Non-polymers , 6 types, 231 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO3 / SULFITE ION / Sulfite


Mass: 80.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO3
#5: Chemical ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.63 Å3/Da / Density % sol: 53.21 % / Description: Orthorhombic
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.5
Details: 0.01 M Co(II)Cl2 hexahydrate, 0.1 M MES monohydrate pH 6.5, 1.8 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 20, 2020 / Details: VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.09→82.13 Å / Num. obs: 24055 / % possible obs: 100 % / Redundancy: 10 % / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.032 / Rrim(I) all: 0.103 / Net I/σ(I): 19.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.09-2.159.50.4491737118380.9290.1520.4745.4100
9.1-81.998.60.04129613440.9990.0140.04347.799.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.09 Å81.99 Å
Translation6.09 Å81.99 Å

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Processing

Software
NameVersionClassification
HKL-30003000data collection
MOSFLM7.3.0data reduction
Aimless0.7.4data scaling
REFMAC2.8.3phasing
Coot0.9.4.1model building
REFMAC5.8.0267refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7F6E

7f6e


Resolution: 2.09→82.13 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.895 / SU ML: 0.106 / SU R Cruickshank DPI: 0.1695 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2141 1097 4.6 %RANDOM
Rwork0.1559 ---
obs0.1586 22957 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.21 Å2 / Biso mean: 27.009 Å2 / Biso min: 9.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å2-0 Å20 Å2
2--0.4 Å2-0 Å2
3---0.24 Å2
Refinement stepCycle: final / Resolution: 2.09→82.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2656 0 57 219 2932
Biso mean--44.12 35.81 -
Num. residues----337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0132771
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172648
X-RAY DIFFRACTIONr_angle_refined_deg1.9481.6493747
X-RAY DIFFRACTIONr_angle_other_deg1.5021.5766062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2135340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.58420.588153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.48815447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0421526
X-RAY DIFFRACTIONr_chiral_restr0.0940.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023116
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02680
LS refinement shellResolution: 2.09→2.142 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.23 82 -
Rwork0.186 1655 -
obs--99.94 %
Refinement TLS params.Method: refined / Origin x: 4.6972 Å / Origin y: 36.6943 Å / Origin z: 28.6651 Å
111213212223313233
T0.1379 Å20.0089 Å20.0356 Å2-0.0239 Å20.0218 Å2--0.0275 Å2
L0.3017 °20.1521 °20.3036 °2-1.9032 °20.592 °2--2.1253 °2
S-0.046 Å °0.0452 Å °0.0109 Å °0.2636 Å °-0.0388 Å °0.0051 Å °0.3549 Å °0.0695 Å °0.0848 Å °

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