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- PDB-7f6k: Crystal structure of metal-citrate-binding protein (MctA) of ABC ... -

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Basic information

Entry
Database: PDB / ID: 7f6k
TitleCrystal structure of metal-citrate-binding 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 / ACETATE ION / CITRIC ACID / CARBON DIOXIDE / Iron ABC transporter, periplasmic iron-binding protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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)116,25122
Polymers114,5503
Non-polymers1,70119
Water8,647480
1
A: Iron ABC transporter, periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,91310
Polymers38,1831
Non-polymers7299
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)38,9279
Polymers38,1831
Non-polymers7448
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)38,4113
Polymers38,1831
Non-polymers2282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.550, 145.110, 79.240
Angle α, β, γ (deg.)90.000, 100.440, 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:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERVALVALAA3 - 3375 - 339
221SERSERVALVALBB3 - 3375 - 339
132ASPASPALAALAAA8 - 33610 - 338
242ASPASPALAALACC8 - 33610 - 338
153ASPASPALAALABB8 - 33610 - 338
263ASPASPALAALACC8 - 33610 - 338

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, 499 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO2
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / 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: 2.29 Å3/Da / Density % sol: 46.4 % / Description: Monoclinic
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.5
Details: 0.2 M ammonium sulphate, 0.1 M MES mohohydrate pH 6.5, 30% (w/v) PEG monoethyl 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: Nov 15, 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: 2.1→77.93 Å / Num. obs: 58898 / % possible obs: 100 % / Redundancy: 3.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.063 / Rrim(I) all: 0.122 / Net I/σ(I): 9.2 / Num. measured all: 213306 / Scaling rejects: 27
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
2.1-2.163.40.4391575545700.8330.2780.5222.899.7
9.15-77.933.60.03926307370.9970.0240.0462299.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.08 Å72.55 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: 2.1→72.66 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / SU B: 9.485 / SU ML: 0.128 / SU R Cruickshank DPI: 0.2267 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.227 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2129 2893 4.9 %RANDOM
Rwork0.1693 ---
obs0.1715 55970 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 155.06 Å2 / Biso mean: 41.639 Å2 / Biso min: 12.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å2-0 Å20.96 Å2
2--0.15 Å20 Å2
3----0.64 Å2
Refinement stepCycle: final / Resolution: 2.1→72.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7902 0 102 480 8484
Biso mean--41.72 34.2 -
Num. residues----1003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0138243
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177893
X-RAY DIFFRACTIONr_angle_refined_deg1.681.64911191
X-RAY DIFFRACTIONr_angle_other_deg1.4081.57618085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.71351024
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.93920.588459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.259151346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1221578
X-RAY DIFFRACTIONr_chiral_restr0.0780.21050
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029361
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022039
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A111660.07
12B111660.07
21A108020.09
22C108020.09
31B108680.08
32C108680.08
LS refinement shellResolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 224 -
Rwork0.226 4120 -
all-4344 -
obs--99.68 %
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)
10.8018-0.33340.220.6041-0.27691.0153-0.01560.1043-0.0317-0.0346-0.0358-0.02790.10070.01970.05150.0388-0.00850.03720.079-0.00540.03911.298912.732110.7411
20.83420.1167-0.2130.86920.12440.5298-0.0685-0.14050.07560.05210.04770.04560.03-0.01130.02090.01650.02960.00080.0983-0.01740.01791.141530.339943.1179
32.7664-0.3204-1.06732.38761.20412.9066-0.6245-0.1995-0.63960.11590.0458-0.180.93830.20170.57880.49890.1320.30290.12860.10530.313421.677859.62898.1116
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 338
2X-RAY DIFFRACTION2B3 - 339
3X-RAY DIFFRACTION3C8 - 337

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