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- PDB-7f6n: Crystal structure of metal-citrate-binding mutant (S26A) protein ... -

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Basic information

Entry
Database: PDB / ID: 7f6n
TitleCrystal structure of metal-citrate-binding mutant (S26A) protein (MctA) of ABC transporter endogenously bound to Mg2+-citrate complex
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 / DI(HYDROXYETHYL)ETHER / 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: 2.3 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)115,90018
Polymers114,5023
Non-polymers1,39815
Water5,531307
1
A: Iron ABC transporter, periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4904
Polymers38,1671
Non-polymers3233
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)38,7207
Polymers38,1671
Non-polymers5536
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)38,6907
Polymers38,1671
Non-polymers5236
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.510, 142.920, 79.270
Angle α, β, γ (deg.)90.000, 100.510, 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: 38167.410 Da / Num. of mol.: 3 / Mutation: S26A
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, 322 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PGR / R-1,2-PROPANEDIOL


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


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.21 Å3/Da / Density % sol: 44.34 % / Description: Monoclinic
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium fluoride, 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: Jan 28, 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: 2.3→77.94 Å / Num. obs: 43237 / % possible obs: 100 % / Redundancy: 4.5 % / CC1/2: 0.974 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.098 / Rrim(I) all: 0.211 / Net I/σ(I): 7.7 / Num. measured all: 194948 / Scaling rejects: 852
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
2.3-2.384.50.5281901242600.770.2840.6012.9100
8.91-77.944.40.12633517630.980.0660.14313.299.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.28 Å71.46 Å
Translation4.28 Å71.46 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: 2.3→71.56 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.9 / SU B: 17.094 / SU ML: 0.205 / SU R Cruickshank DPI: 0.4757 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.476 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2423 2114 4.9 %RANDOM
Rwork0.1945 ---
obs0.1969 41074 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.67 Å2 / Biso mean: 29.314 Å2 / Biso min: 6.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0.08 Å2
2--0.07 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 2.3→71.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7941 0 91 307 8339
Biso mean--33.35 26.18 -
Num. residues----1008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0138216
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177887
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.6511130
X-RAY DIFFRACTIONr_angle_other_deg1.3371.57618052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.99951011
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80120.439456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.612151336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8861579
X-RAY DIFFRACTIONr_chiral_restr0.0770.21048
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029309
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022033
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A110580.07
12B110580.07
21A108700.08
22C108700.08
31B109710.08
32C109710.08
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 146 -
Rwork0.24 3061 -
all-3207 -
obs--100 %
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)
10.6305-0.32260.26950.7025-0.4080.9431-0.00270.0551-0.0367-0.0029-0.0183-0.02540.0296-0.04560.0210.0445-0.01890.03580.113-0.01440.03411.191616.381710.6742
20.7260.26530.00871.49830.14250.394-0.0736-0.06180.09460.03040.04580.0451-0.0034-0.0490.02780.04180.03020.00540.1095-0.01240.02971.048433.553143.1437
33.5052-0.5352-0.77520.810.18841.3744-0.0936-0.1696-0.6650.0593-0.0168-0.0250.20120.11630.11040.03740.01910.00610.02050.03770.148721.41962.05198.1119
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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