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- PDB-7f6e: Crystal structure of metal-citrate-binding protein (MctA) of ABC ... -

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Basic information

Entry
Database: PDB / ID: 7f6e
TitleCrystal structure of metal-citrate-binding protein (MctA) of ABC transporter endogenously bound to Mg2+-citrate complex (Form I)
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 / (2S)-2-HYDROXYPROPANOIC ACID / CITRIC ACID / CARBON DIOXIDE / S-1,2-PROPANEDIOL / Iron ABC transporter, periplasmic iron-binding protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.77 Å
AuthorsKanaujia, S.P. / Mandal, S.K. / Gogoi, P.
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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Iron ABC transporter, periplasmic iron-binding protein
B: Iron ABC transporter, periplasmic iron-binding protein
C: Iron ABC transporter, periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,45546
Polymers114,5503
Non-polymers2,90543
Water12,899716
1
A: Iron ABC transporter, periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,43120
Polymers38,1831
Non-polymers1,24719
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Iron ABC transporter, periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,44021
Polymers38,1831
Non-polymers1,25720
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Iron ABC transporter, periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5845
Polymers38,1831
Non-polymers4014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.270, 144.250, 79.150
Angle α, β, γ (deg.)90.000, 100.160, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

End auth comp-ID: VAL / End label comp-ID: VAL

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETAA-1 - 3371 - 339
221METMETBB-1 - 3371 - 339
132SERSERAA3 - 3375 - 339
242SERSERCC3 - 3375 - 339
153SERSERBB3 - 3375 - 339
263SERSERCC3 - 3375 - 339

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 38183.410 Da / Num. of mol.: 3
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, 759 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CO2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-2OP / (2S)-2-HYDROXYPROPANOIC ACID


Mass: 90.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6O3
#9: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 716 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.23 Å3/Da / Density % sol: 44.98 % / Description: Monoclinic
Crystal growTemperature: 293 K / Method: microbatch / pH: 5.5
Details: 0.1 M sodium citrate tribasic dihydrate pH 5.5, 16% 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: Oct 21, 2017 / Details: VariMax HF
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.77→52.98 Å / Num. obs: 92348 / % possible obs: 95.8 % / Redundancy: 5.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.03 / Rrim(I) all: 0.072 / Net I/σ(I): 15.2
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
1.77-1.850.4112149142780.8790.1980.4583.388.9
9.71-52.935.40.02933216130.9990.0130.03236.499.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.32 Å52.93 Å
Translation4.32 Å52.93 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: 3C9H

3c9h


Resolution: 1.77→52.98 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.831 / SU ML: 0.061 / SU R Cruickshank DPI: 0.1042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1715 4480 4.9 %RANDOM
Rwork0.1368 ---
obs0.1385 87826 95.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.75 Å2 / Biso mean: 23.425 Å2 / Biso min: 8.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20.38 Å2
2---0.22 Å20 Å2
3----0.34 Å2
Refinement stepCycle: final / Resolution: 1.77→52.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8016 0 179 716 8911
Biso mean--33.07 32.17 -
Num. residues----1017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0138423
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178107
X-RAY DIFFRACTIONr_angle_refined_deg1.8111.65311394
X-RAY DIFFRACTIONr_angle_other_deg1.5551.57518568
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.30951044
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.2920.472466
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.137151380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.751581
X-RAY DIFFRACTIONr_chiral_restr0.0940.21070
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.029510
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022076
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A114710.07
12B114710.07
21A111210.09
22C111210.09
31B111160.09
32C111160.09
LS refinement shellResolution: 1.77→1.819 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.219 292 -
Rwork0.203 6108 -
obs--89.12 %
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)
10.4774-0.17350.08760.3727-0.18160.6694-0.01840.0402-0.0229-0.004-0.0131-0.02280.0483-0.02060.03150.0448-0.0140.00160.0378-0.00730.04311.684512.798610.8335
20.56040.1309-0.12040.67680.0980.3546-0.047-0.06350.05440.02390.02330.0409-0.001-0.01780.02380.0460.0188-0.02590.0549-0.00790.03541.23830.214643.2529
31.7815-0.3257-0.84330.59330.32991.3953-0.2395-0.097-0.33380.09960.02350.01960.28190.08010.2160.1360.03170.05470.01270.03340.112521.868359.48228.1539
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 338
2X-RAY DIFFRACTION2B-1 - 339
3X-RAY DIFFRACTION3C3 - 338

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