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- PDB-7f6u: Crystal structure of metal-citrate-binding mutant (Y221A) protein... -

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Basic information

Entry
Database: PDB / ID: 7f6u
TitleCrystal structure of metal-citrate-binding mutant (Y221A) 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 / homology
Function and homology information


outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
2-(hydroxymethyl)butane-1,4-diol / 2-HYDROXY BUTANE-1,4-DIOL / CACODYLATE ION / CARBON DIOXIDE / DI(HYDROXYETHYL)ETHER / Iron ABC transporter, periplasmic iron-binding protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 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)38,99413
Polymers38,0911
Non-polymers90312
Water5,062281
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-10 kcal/mol
Surface area13950 Å2
Unit cell
Length a, b, c (Å)44.420, 108.610, 163.170
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-650-

HOH

21A-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: 38091.316 Da / Num. of mol.: 1 / Mutation: Y221A
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 , 9 types, 293 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-BGQ / 2-HYDROXY BUTANE-1,4-DIOL


Mass: 105.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9O3
#8: Chemical ChemComp-1MI / 2-(hydroxymethyl)butane-1,4-diol


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3
#9: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.61 Å3/Da / Density % sol: 52.87 % / Description: Orthorhombic
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.5
Details: 0.2 M ammonium sulfate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 30% (w/v) PEG 8000

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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: Aug 9, 2019 / Details: VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→54.3 Å / Num. obs: 40385 / % possible obs: 100 % / Redundancy: 8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.032 / Rrim(I) all: 0.093 / Net I/σ(I): 13.2 / Num. measured all: 324728 / Scaling rejects: 159
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
1.75-1.787.60.5011670621900.9070.1920.5372.5100
9.09-54.37.20.05324523410.9980.0210.05725.499.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.03 Å48.63 Å

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Processing

Software
NameVersionClassification
HKL-30003000data collection
MOSFLM7.3.0data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
Coot0.9.4.1model building
REFMAC5.8.0267refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7F6E

7f6e


Resolution: 1.75→48.68 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.76 / SU ML: 0.092 / SU R Cruickshank DPI: 0.1231 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2362 1985 4.9 %RANDOM
Rwork0.2039 ---
obs0.2054 38399 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.82 Å2 / Biso mean: 29.588 Å2 / Biso min: 13.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å2-0 Å2
2---0.23 Å2-0 Å2
3---0.5 Å2
Refinement stepCycle: final / Resolution: 1.75→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2667 0 53 281 3001
Biso mean--48.26 37.17 -
Num. residues----339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0132798
X-RAY DIFFRACTIONr_bond_other_d0.0060.0172705
X-RAY DIFFRACTIONr_angle_refined_deg2.1341.6583786
X-RAY DIFFRACTIONr_angle_other_deg1.5421.5886195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0475348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.14820.577156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5415458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2881527
X-RAY DIFFRACTIONr_chiral_restr0.0940.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023154
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02688
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 153 -
Rwork0.288 2799 -
all-2952 -
obs--99.97 %
Refinement TLS params.Method: refined / Origin x: 4.8149 Å / Origin y: 37.0978 Å / Origin z: 28.8343 Å
111213212223313233
T0.1257 Å20.0126 Å20.0274 Å2-0.0559 Å20.0277 Å2--0.0186 Å2
L0.2054 °20.1394 °20.1233 °2-1.7063 °20.9842 °2--2.1333 °2
S-0.0672 Å °0.0646 Å °0.0255 Å °0.2158 Å °-0.0194 Å °0.0645 Å °0.2857 Å °0.0867 Å °0.0866 Å °

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