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- PDB-4pm4: Structure of a putative periplasmic iron siderophore binding prot... -

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Basic information

Entry
Database: PDB / ID: 4pm4
TitleStructure of a putative periplasmic iron siderophore binding protein (Rv0265c) from Mycobacterium tuberculosis H37Rv
ComponentsIron complex transporter substrate-binding protein
KeywordsSOLUTE-BINDING PROTEIN / periplasmic / binding protein / siderophore / Structural Genomics / PSI-2 / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


: / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable periplasmic iron-transport lipoprotein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsArbing, M.A. / Chan, S. / Tran, N. / Kuo, E. / Lu, J. / Harris, L.R. / Zhou, T.T. / Eisenberg, D. / TB Structural Genomics Consortium (TBSGC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI068135 United States
CitationJournal: To Be Published
Title: Structure of a putative periplasmic iron siderophore binding protein (Rv0265c) from Mycobacterium tuberculosis H37Rv
Authors: Arbing, M.A. / Chan, S. / Tran, N. / Kuo, E. / Lu, J. / Harris, L.R. / Zhou, T.T. / Eisenberg, D.
History
DepositionMay 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Iron complex transporter substrate-binding protein
B: Iron complex transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9057
Polymers65,6072
Non-polymers2985
Water4,234235
1
A: Iron complex transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1026
Polymers32,8031
Non-polymers2985
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Iron complex transporter substrate-binding protein


Theoretical massNumber of molelcules
Total (without water)32,8031
Polymers32,8031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.551, 65.434, 72.330
Angle α, β, γ (deg.)90.00, 116.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Iron complex transporter substrate-binding protein / Probable periplasmic iron-transport lipoprotein


Mass: 32803.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv0265c, RVBD_0265c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: L7N6B2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 45.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Reservoir solution: 3.0 M ammonium sulfate, 95 mM citric acid pH 5.0. Protein buffer: 20 mM Tris, pH 8.0, 300 mM NaCl, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 13, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 68787 / Num. obs: 28285 / % possible obs: 94.5 % / Redundancy: 2.4 % / Rsym value: 0.127 / Net I/σ(I): 10.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.3 / % possible all: 98.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1555) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MDY

4mdy


Resolution: 2.2→29.204 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2517 1406 4.98 %Random selection
Rwork0.203 ---
obs0.2055 28260 93.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→29.204 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4411 0 13 235 4659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034521
X-RAY DIFFRACTIONf_angle_d0.7876181
X-RAY DIFFRACTIONf_dihedral_angle_d12.1631609
X-RAY DIFFRACTIONf_chiral_restr0.031709
X-RAY DIFFRACTIONf_plane_restr0.004807
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1914-2.26970.31251410.26582697X-RAY DIFFRACTION94
2.2697-2.36050.29981520.24592724X-RAY DIFFRACTION98
2.3605-2.46790.27271270.23222799X-RAY DIFFRACTION98
2.4679-2.59790.26641600.22682785X-RAY DIFFRACTION98
2.5979-2.76060.28681530.2212761X-RAY DIFFRACTION98
2.7606-2.97350.26481570.21972752X-RAY DIFFRACTION97
2.9735-3.27240.2711320.20962722X-RAY DIFFRACTION95
3.2724-3.74510.23511270.19142590X-RAY DIFFRACTION91
3.7451-4.71520.21220.15722514X-RAY DIFFRACTION87
4.7152-29.20.23161350.18592510X-RAY DIFFRACTION86
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)
12.00280.07450.08981.6466-0.29351.25410.1611-0.1754-0.07330.26490.05560.45290.0788-0.3665-0.04220.1885-0.03280.02540.26680.04410.3629-8.452615.727436.2413
22.5247-0.98330.09662.60060.07762.17410.22060.4075-0.0848-0.1706-0.16930.14890.07290.0464-0.02180.25850.0076-0.04710.178-0.05920.241610.0144.550418.5878
32.0873-1.91940.10832.8318-0.29260.90210.13120.0881-0.0957-0.2012-0.12390.03210.05910.0653-0.03120.18490.0141-0.02520.1664-0.01280.203114.95043.914125.5188
42.94930.0024-0.98061.4314-1.31281.9559-0.12360.39160.6461-0.38860.3940.41820.095-0.2904-0.10750.3562-0.0344-0.06070.28870.10130.43990.48236.140710.0627
51.25390.1392-0.8981.32850.03491.5149-0.25270.6153-0.2921-0.80420.10530.08640.618-0.2450.30111.0003-0.22670.12340.4478-0.0690.31279.96519.472-2.3592
62.75760.0127-0.311.2946-0.31281.6981-0.17630.20030.0401-0.356-0.1159-0.4310.37890.35510.21320.50730.00530.19140.34860.05930.334826.553225.27179.6205
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 15:158)
2X-RAY DIFFRACTION2(chain A and resid 159:187)
3X-RAY DIFFRACTION3(chain A and resid 188:304)
4X-RAY DIFFRACTION4(chain B and resid 15:143)
5X-RAY DIFFRACTION5(chain B and resid 144:177)
6X-RAY DIFFRACTION6(chain B and resid 178:303)

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