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- PDB-7f6o: Crystal structure of metal-citrate-binding mutant (S26A) protein ... -

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Basic information

Entry
Database: PDB / ID: 7f6o
TitleCrystal structure of metal-citrate-binding mutant (S26A) protein (MctA) of ABC transporter endogenously bound to Mn2+-citrate complex
ComponentsIron ABC transporter, periplasmic iron-binding protein
KeywordsTRANSPORT PROTEIN / Substrate-binding protein / metal ion / secondary transporter / symporter
Function / homology
Function and homology information


outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
CITRIC ACID / : / DI(HYDROXYETHYL)ETHER / SULFUR DIOXIDE / SULFITE ION / Iron ABC transporter, periplasmic iron-binding protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)77,82417
Polymers76,3352
Non-polymers1,48915
Water3,279182
1
A: Iron ABC transporter, periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0019
Polymers38,1671
Non-polymers8348
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)38,8238
Polymers38,1671
Non-polymers6557
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.730, 100.130, 143.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / 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-IDAuth asym-IDLabel asym-ID
11AA
22BB

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 38167.410 Da / Num. of mol.: 2 / 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 , 10 types, 197 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Chemical ChemComp-SO2 / SULFUR DIOXIDE


Mass: 64.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2S
#10: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.14 Å3/Da / Density % sol: 42.68 % / Description: Orthorhombic
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: Aug 2, 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: 2.5→71.65 Å / Num. obs: 23063 / % possible obs: 99.9 % / Redundancy: 7.3 % / CC1/2: 0.971 / Rmerge(I) obs: 0.23 / Rpim(I) all: 0.092 / Rrim(I) all: 0.248 / Net I/σ(I): 6.4 / Num. measured all: 168215 / Scaling rejects: 243
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
2.5-2.67.10.5641786225260.8620.2270.61399.7
9.01-71.656.70.13538735740.980.0570.1479.499.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.66 Å58.28 Å
Translation6.66 Å58.28 Å

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Processing

Software
NameVersionClassification
HKL-30003000data collection
MOSFLM7.3.0data reduction
Aimless0.7.4data scaling
PHASER3.8.3phasing
Coot0.9.4.1model building
REFMAC5.8.0267refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7F6E

7f6e


Resolution: 2.5→58.28 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.858 / SU B: 15.55 / SU ML: 0.183 / SU R Cruickshank DPI: 0.0534 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2652 1160 5 %RANDOM
Rwork0.194 ---
obs0.1975 21869 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.45 Å2 / Biso mean: 18.819 Å2 / Biso min: 2.18 Å2
Baniso -1Baniso -2Baniso -3
1--6.25 Å2-0 Å2-0 Å2
2--18.08 Å20 Å2
3----11.83 Å2
Refinement stepCycle: final / Resolution: 2.5→58.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5294 0 87 182 5563
Biso mean--32.45 18.38 -
Num. residues----672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0135509
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175274
X-RAY DIFFRACTIONr_angle_refined_deg1.7821.6517459
X-RAY DIFFRACTIONr_angle_other_deg1.3411.57612073
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5135676
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90620.358307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.72815894
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6891554
X-RAY DIFFRACTIONr_chiral_restr0.080.2699
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026221
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021363
Refine LS restraints NCS

Ens-ID: 1 / Number: 10872 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 83 -
Rwork0.245 1553 -
all-1636 -
obs--99.76 %
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)
10.6071-0.07380.06161.401-0.10230.8261-0.02020.0269-0.033-0.00690.01420.0297-0.0250.00860.0060.0088-0.01720.00690.0456-0.0090.0113-64.720365.8249-58.731
20.5899-0.2396-0.18520.67630.46361.7909-0.04180.0463-0.0295-0.0285-0.03110.0567-0.136-0.07140.07290.024-0.0079-0.01410.01690.00750.0182-35.221829.1393-46.5445
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 338
2X-RAY DIFFRACTION2B3 - 338

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