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- PDB-7f6s: Crystal structure of metal-citrate-binding mutant (T199A) protein... -

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Basic information

Entry
Database: PDB / ID: 7f6s
TitleCrystal structure of metal-citrate-binding mutant (T199A) 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 / outer membrane-bounded periplasmic space / metal ion binding / CARBON DIOXIDE / GLYCOLIC ACID / DI(HYDROXYETHYL)ETHER / Iron ABC transporter, periplasmic iron-binding protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 2.1Nov 29, 2023Group: Refinement description / Category: 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)38,76010
Polymers38,1531
Non-polymers6079
Water4,252236
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-6 kcal/mol
Surface area14070 Å2
Unit cell
Length a, b, c (Å)44.290, 108.850, 163.570
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-639-

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: 38153.387 Da / Num. of mol.: 1 / Mutation: T199A
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, 245 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#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.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-GOA / GLYCOLIC ACID / HYDROXYACETIC ACID / HYDROXYETHANOIC ACID


Mass: 76.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 7
Details: 0.2 M ammonium tartrate dibasic pH 7.0, 20% PEG 3350

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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: Jul 24, 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: 1.8→48.8 Å / Num. obs: 37221 / % possible obs: 100 % / Redundancy: 9.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.023 / Rrim(I) all: 0.073 / Net I/σ(I): 19
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
1.8-1.849.40.4872043621790.9410.1650.5143.8100
9-48.758.40.0429723550.9990.0140.04337.699.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.04 Å48.75 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: 1.8→48.8 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.242 / SU ML: 0.065 / SU R Cruickshank DPI: 0.0986 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1816 1851 5 %RANDOM
Rwork0.1513 ---
obs0.1528 35370 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: 83.23 Å2 / Biso mean: 28.577 Å2 / Biso min: 12.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å2-0 Å2
2--0.25 Å20 Å2
3----0.4 Å2
Refinement stepCycle: final / Resolution: 1.8→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2672 0 38 236 2946
Biso mean--51.09 38.39 -
Num. residues----339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0132794
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172706
X-RAY DIFFRACTIONr_angle_refined_deg2.1451.6523781
X-RAY DIFFRACTIONr_angle_other_deg1.5811.5786194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2485348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.12320.318157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83315460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5651528
X-RAY DIFFRACTIONr_chiral_restr0.1070.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023159
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02697
LS refinement shellResolution: 1.8→1.84 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.215 136 -
Rwork0.2 2577 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 4.8368 Å / Origin y: 37.1827 Å / Origin z: 28.832 Å
111213212223313233
T0.0735 Å20.0085 Å20.0206 Å2-0.0401 Å20.024 Å2--0.0181 Å2
L0.3124 °20.1594 °20.1596 °2-1.2817 °20.6169 °2--1.6225 °2
S-0.0471 Å °0.0721 Å °0.0332 Å °0.107 Å °-0.02 Å °0.0308 Å °0.2283 Å °0.0359 Å °0.0671 Å °

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