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- PDB-7fhp: Crystal structure of an orphan heme uptake protein (MhuP) of ABC ... -

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Basic information

Entry
Database: PDB / ID: 7fhp
TitleCrystal structure of an orphan heme uptake protein (MhuP) of ABC transporter from Mycobacterium tuberculosis (Form II)
ComponentsProbable periplasmic iron-transport lipoprotein
KeywordsTRANSPORT PROTEIN / Hemoglobin / Iron homeostasis / Nutritional immunity / substrate-binding protein / nucleotide-binding domain
Function / homology: / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Prokaryotic membrane lipoprotein lipid attachment site profile. / SULFITE ION / Probable periplasmic iron-transport lipoprotein
Function and homology information
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å
AuthorsMandal, S.K. / Kanaujia, S.P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR16065/NER/95/61/2015 India
CitationJournal: Int.J.Biol.Macromol. / Year: 2022
Title: Role of an orphan substrate-binding protein MhuP in transient heme transfer in Mycobacterium tuberculosis
Authors: Mandal, S.K. / Kanaujia, S.P.
History
DepositionJul 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Jun 15, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Nov 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: Probable periplasmic iron-transport lipoprotein
B: Probable periplasmic iron-transport lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,91110
Polymers65,2422
Non-polymers6698
Water11,187621
1
A: Probable periplasmic iron-transport lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0446
Polymers32,6211
Non-polymers4225
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-16 kcal/mol
Surface area13250 Å2
MethodPISA
2
B: Probable periplasmic iron-transport lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8674
Polymers32,6211
Non-polymers2463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.380, 39.670, 92.970
Angle α, β, γ (deg.)90.000, 113.380, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 8 - 299 / Label seq-ID: 8 - 299

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Probable periplasmic iron-transport lipoprotein


Mass: 32621.182 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: Rv0265c / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: L7N6B2

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Non-polymers , 5 types, 629 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 621 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.71 Å3/Da / Density % sol: 54.59 %
Description: Monoclinic THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2 M lithium sulfate monohydrate, 0.1 M sodium acetate trihydrate pH 4.6, 30% (w/v) 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: Jan 1, 2020 / Details: Vari Max HF
RadiationMonochromator: Ni / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→53.25 Å / Num. obs: 45608 / % possible obs: 99 % / Redundancy: 3.9 % / CC1/2: 0.985 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.067 / Rrim(I) all: 0.135 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.01-2.063.30.2932410.8970.1770.34296.1
8.98-53.253.60.0825840.980.0520.09899.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.95 Å53.2 Å
Translation4.95 Å53.2 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: 7FHM

7fhm


Resolution: 2.01→53.25 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.919 / SU B: 7.035 / SU ML: 0.105 / SU R Cruickshank DPI: 0.1679 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2152 2243 4.9 %RANDOM
Rwork0.1714 ---
obs0.1737 43355 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.31 Å2 / Biso mean: 20.875 Å2 / Biso min: 8.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å2-0 Å20.84 Å2
2---1.33 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: final / Resolution: 2.01→53.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4476 0 41 621 5138
Biso mean--40.44 29.03 -
Num. residues----584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0134660
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174513
X-RAY DIFFRACTIONr_angle_refined_deg1.7851.636368
X-RAY DIFFRACTIONr_angle_other_deg1.4581.57810356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6745600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04922.361233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89615728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3831531
X-RAY DIFFRACTIONr_chiral_restr0.0890.2623
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025334
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021060
Refine LS restraints NCS

Ens-ID: 1 / Number: 9178 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.01→2.059 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.264 154 -
Rwork0.201 3081 -
obs--95.65 %
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)
10.6349-0.038-0.07540.34330.04830.42160.0120.0018-0.0504-0.0405-0.00860.0052-0.0251-0.0213-0.00340.05340.00930.00110.04440.00420.004631.990511.120628.8858
20.667-0.0760.16321.1557-0.21130.6006-0.0035-0.03390.06250.02630.04040.1653-0.0315-0.0697-0.03690.0032-0.00370.00740.0504-0.01030.038226.59255.1072-6.1613
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 299
2X-RAY DIFFRACTION2B8 - 299

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