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- PDB-7f6q: Crystal structure of metal-citrate-binding mutant (S79A) protein ... -

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Basic information

Entry
Database: PDB / ID: 7f6q
TitleCrystal structure of metal-citrate-binding mutant (S79A) 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
ACETATE ION / CARBON DIOXIDE / 1,3-PROPANDIOL / DI(HYDROXYETHYL)ETHER / SULFUR DIOXIDE / Iron ABC transporter, periplasmic iron-binding protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.63 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)38,98315
Polymers38,1671
Non-polymers81614
Water6,395355
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-21 kcal/mol
Surface area14100 Å2
Unit cell
Length a, b, c (Å)72.170, 72.170, 114.300
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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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: S79A
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 , 8 types, 369 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO2 / SULFUR DIOXIDE


Mass: 64.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2S
#4: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.28 Å3/Da / Density % sol: 46.1 % / Description: Trigonal
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.5
Details: 0.2 M ammonium sulphate, 0.1 M MES monohydrate pH 6.5, 30% (w/v) PEG monomethyl ether 5000

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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 8, 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: 1.63→42.21 Å / Num. obs: 43745 / % possible obs: 100 % / Redundancy: 10.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.017 / Rrim(I) all: 0.057 / Net I/σ(I): 24.7
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
1.63-1.669.70.2312041421130.9790.0770.2445.199.5
8.92-42.189.20.017292131810.0060.01847.899.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.87 Å42.18 Å
Translation5.87 Å42.18 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: 1.63→42.21 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.551 / SU ML: 0.062 / SU R Cruickshank DPI: 0.0955 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2132 2174 5 %RANDOM
Rwork0.1755 ---
obs0.1772 41528 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.11 Å2 / Biso mean: 23.607 Å2 / Biso min: 11.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å2-0 Å2
3----0.52 Å2
Refinement stepCycle: final / Resolution: 1.63→42.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2665 0 47 355 3067
Biso mean--38.02 34.43 -
Num. residues----338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0132829
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172746
X-RAY DIFFRACTIONr_angle_refined_deg2.2181.6543834
X-RAY DIFFRACTIONr_angle_other_deg1.6261.5776294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5395359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.0720.44159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61215468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2441528
X-RAY DIFFRACTIONr_chiral_restr0.1090.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023213
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02703
LS refinement shellResolution: 1.63→1.671 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.22 162 -
Rwork0.2 3026 -
obs--99.63 %
Refinement TLS params.Method: refined / Origin x: -29.4986 Å / Origin y: 12.3535 Å / Origin z: 3.8802 Å
111213212223313233
T0.062 Å2-0.0203 Å20.0222 Å2-0.0246 Å2-0.0087 Å2--0.0398 Å2
L0.5924 °2-0.1562 °20.2306 °2-0.6945 °20.0503 °2--0.2497 °2
S-0.0288 Å °-0.0244 Å °-0.0413 Å °-0.0346 Å °0.0498 Å °-0.1194 Å °-0.0282 Å °-0.0334 Å °-0.021 Å °

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