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- PDB-7f6p: Crystal structure of metal-citrate-binding mutant (D28A) protein ... -

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Basic information

Entry
Database: PDB / ID: 7f6p
TitleCrystal structure of metal-citrate-binding mutant (D28A) protein (MctA) of ABC transporter endogenously bound to citrate
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 / CITRIC ACID / CARBON DIOXIDE / 1,3-PROPANDIOL / R-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: 2.15 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 ...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)115,43913
Polymers114,4183
Non-polymers1,02110
Water8,143452
1
A: Iron ABC transporter, periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6567
Polymers38,1391
Non-polymers5166
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)38,4524
Polymers38,1391
Non-polymers3123
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)38,3322
Polymers38,1391
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.310, 146.260, 79.090
Angle α, β, γ (deg.)90.000, 99.890, 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:

Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 3 - 338 / Label seq-ID: 5 - 340

Dom-IDComponent-IDEns-IDAuth asym-IDLabel asym-ID
111AA
221BB
132AA
242CC
153BB
263CC

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: 38139.402 Da / Num. of mol.: 3 / Mutation: D28A
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, 462 molecules

#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#5: Chemical ChemComp-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#6: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / 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: 2.3 Å3/Da / Density % sol: 46.59 % / Description: Monoclinic
Crystal growTemperature: 293 K / Method: microbatch / Details: 0.2 M ammonium phosphate dibasic, 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: Dec 29, 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: 2.15→73.24 Å / Num. obs: 52451 / % possible obs: 95.5 % / Redundancy: 5.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.041 / Rrim(I) all: 0.1 / Net I/σ(I): 12.7
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
2.15-2.215.30.5962175640810.8510.2710.6563.191.4
9.12-73.135.60.03141797410.9980.0140.03429.699.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.11 Å73.13 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: 2.15→73.24 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.824 / SU ML: 0.129 / SU R Cruickshank DPI: 0.2817 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.282 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2144 2565 4.9 %RANDOM
Rwork0.1737 ---
obs0.1757 49852 95.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 191.22 Å2 / Biso mean: 52.468 Å2 / Biso min: 8.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å2-0 Å20.14 Å2
2--1.72 Å20 Å2
3----1.18 Å2
Refinement stepCycle: final / Resolution: 2.15→73.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7935 0 68 452 8455
Biso mean--49.46 37.34 -
Num. residues----1008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0138203
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177877
X-RAY DIFFRACTIONr_angle_refined_deg1.7081.65111120
X-RAY DIFFRACTIONr_angle_other_deg1.421.57618024
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7651013
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94220.263456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.746151340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3381581
X-RAY DIFFRACTIONr_chiral_restr0.0850.21049
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029310
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022044
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A11146
12B11146
21A11016
22C11016
31B11017
32C11017
LS refinement shellResolution: 2.15→2.21 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.247 182 -
Rwork0.215 3481 -
obs--91.19 %
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)
11.2426-0.52110.28480.6875-0.40451.5658-0.01680.1662-0.0321-0.0602-0.089-0.06330.18980.02240.10580.0522-0.01350.03730.038-0.00660.031711.382612.658811.2302
21.16620.047-0.36191.32530.26960.8191-0.1177-0.25860.16750.09040.0930.04060.0451-0.00410.02470.02240.0439-0.01590.1034-0.04640.03241.645230.454843.3496
33.19230.091-1.04482.03461.53153.7154-0.8494-0.299-0.80790.30610.1004-0.19911.57740.16640.7491.04280.19140.46270.2670.15430.547821.577160.03657.5173
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 338
2X-RAY DIFFRACTION2B3 - 338
3X-RAY DIFFRACTION3C3 - 338

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