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

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Basic information

Entry
Database: PDB / ID: 7fhm
TitleCrystal structure of an orphan heme uptake protein (MhuP) of ABC transporter from Mycobacterium tuberculosis (Form I)
ComponentsProbable periplasmic iron-transport lipoprotein
KeywordsTRANSPORT PROTEIN / Hemoglobin / Iron homeostasis / Nutritional immunity / substrate-binding protein / nucleotide-binding domain
Function / homology
Function and homology information


outer membrane-bounded periplasmic space
Similarity search - Function
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.
Similarity search - Domain/homology
ACETATE ION / CITRIC ACID / CARBON DIOXIDE / CARBONATE ION / Probable periplasmic iron-transport lipoprotein
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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)65,99811
Polymers65,2422
Non-polymers7569
Water12,538696
1
A: Probable periplasmic iron-transport lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0716
Polymers32,6211
Non-polymers4505
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-2 kcal/mol
Surface area13190 Å2
MethodPISA
2
B: Probable periplasmic iron-transport lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9265
Polymers32,6211
Non-polymers3054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-1 kcal/mol
Surface area12940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.340, 39.410, 94.670
Angle α, β, γ (deg.)90.000, 108.340, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 9 - 298 / Label seq-ID: 9 - 298

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 , 7 types, 705 molecules

#2: Chemical ChemComp-CIT / CITRIC ACID


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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#6: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 696 / 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: 2.53 Å3/Da / Density % sol: 51.45 %
Description: Monoclinic THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: microbatch / pH: 5 / Details: 0.1 M citrate pH 5.0 and 20% PEG 6000

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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: Feb 26, 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: 1.8→55.09 Å / Num. obs: 61369 / % possible obs: 100 % / Redundancy: 4.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.037 / Rrim(I) all: 0.082 / Net I/σ(I): 14.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.8-1.844.50.46535640.8190.2450.52799.8
9-55.094.40.0365590.9950.0190.04299.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.91 Å55.03 Å
Translation4.91 Å55.03 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: 4PM4

4pm4


Resolution: 1.8→55.03 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.256 / SU ML: 0.07 / SU R Cruickshank DPI: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1893 3055 5 %RANDOM
Rwork0.1552 ---
obs0.1569 58301 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: 83.47 Å2 / Biso mean: 24.433 Å2 / Biso min: 8.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0 Å20.19 Å2
2---0.42 Å2-0 Å2
3---0.48 Å2
Refinement stepCycle: final / Resolution: 1.8→55.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4466 0 50 696 5212
Biso mean--36.71 31.91 -
Num. residues----583
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0134686
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174552
X-RAY DIFFRACTIONr_angle_refined_deg1.8091.6316403
X-RAY DIFFRACTIONr_angle_other_deg1.511.57810447
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6565605
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.98122.265234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56515741
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8761532
X-RAY DIFFRACTIONr_chiral_restr0.0950.2625
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025376
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021068
Refine LS restraints NCS

Ens-ID: 1 / Number: 9218 / 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: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 210 -
Rwork0.241 4249 -
all-4459 -
obs--99.8 %
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)
10.64620.0038-0.17130.4046-0.04060.52260.01130.08740.002-0.0766-0.0290.0701-0.0238-0.05070.01770.01670.0077-0.01290.0231-0.00910.040119.1265-9.24738.8905
20.8497-0.44570.43491.1145-0.34561.9470.0720.09980.0583-0.1781-0.0151-0.06470.27120.0439-0.05690.05660.00630.00030.03110.01160.0122-11.3985-2.854220.1794
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 299
2X-RAY DIFFRACTION2B9 - 299

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