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- PDB-3may: Crystal structure of a secreted Mycobacterium tuberculosis heme-b... -

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Basic information

Entry
Database: PDB / ID: 3may
TitleCrystal structure of a secreted Mycobacterium tuberculosis heme-binding protein
ComponentsPOSSIBLE EXPORTED PROTEIN
Keywordsheme-binding protein / helical protein
Function / homology
Function and homology information


heme transport / heme binding / extracellular region
Similarity search - Function
Haemophore, haem-binding domain / Hemophore Rv0203 / Haemophore, haem-binding / Haemophore, haem-binding domain superfamily / Haemophore, haem-binding / F1FO ATP Synthase / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
MHB domain-containing protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsGoulding, C.W. / Chim, N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Discovery and characterization of a unique mycobacterial heme acquisition system.
Authors: Tullius, M.V. / Harmston, C.A. / Owens, C.P. / Chim, N. / Morse, R.P. / McMath, L.M. / Iniguez, A. / Kimmey, J.M. / Sawaya, M.R. / Whitelegge, J.P. / Horwitz, M.A. / Goulding, C.W.
History
DepositionMar 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POSSIBLE EXPORTED PROTEIN
B: POSSIBLE EXPORTED PROTEIN
C: POSSIBLE EXPORTED PROTEIN
D: POSSIBLE EXPORTED PROTEIN
E: POSSIBLE EXPORTED PROTEIN
G: POSSIBLE EXPORTED PROTEIN
F: POSSIBLE EXPORTED PROTEIN
H: POSSIBLE EXPORTED PROTEIN


Theoretical massNumber of molelcules
Total (without water)83,2788
Polymers83,2788
Non-polymers00
Water1,00956
1
A: POSSIBLE EXPORTED PROTEIN
B: POSSIBLE EXPORTED PROTEIN
C: POSSIBLE EXPORTED PROTEIN
D: POSSIBLE EXPORTED PROTEIN


Theoretical massNumber of molelcules
Total (without water)41,6394
Polymers41,6394
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8470 Å2
ΔGint-71 kcal/mol
Surface area16900 Å2
MethodPISA
2
E: POSSIBLE EXPORTED PROTEIN
G: POSSIBLE EXPORTED PROTEIN
F: POSSIBLE EXPORTED PROTEIN
H: POSSIBLE EXPORTED PROTEIN


Theoretical massNumber of molelcules
Total (without water)41,6394
Polymers41,6394
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-74 kcal/mol
Surface area17210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.671, 72.671, 173.909
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
POSSIBLE EXPORTED PROTEIN / Rv0203


Mass: 10409.718 Da / Num. of mol.: 8 / Fragment: UNP RESIDUES 36-136
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT0213, Rv0203 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: O53654
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.76 Å3/Da / Density % sol: 55.39 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9792, 0.9795, 1.04
DetectorDate: Jun 15, 2002
RadiationMonochromator: Si III channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97951
31.041
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.51
11-H, K, -L20.49
ReflectionResolution: 2.5→100 Å / Num. obs: 31089 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 14.9 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 31.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
MLPHAREphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→72.68 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.901 / SU B: 17.594 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2557 1595 5.2 %RANDOM
Rwork0.1947 ---
obs0.19776 29261 99.49 %-
all-30856 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.279 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20 Å20 Å2
2--1.69 Å20 Å2
3----3.39 Å2
Refinement stepCycle: LAST / Resolution: 2.5→72.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5323 0 0 56 5379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0215410
X-RAY DIFFRACTIONr_angle_refined_deg1.9791.9727367
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7565735
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.08626.211190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.34515869
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6241516
X-RAY DIFFRACTIONr_chiral_restr0.1340.2894
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214004
X-RAY DIFFRACTIONr_mcbond_it1.4451.53701
X-RAY DIFFRACTIONr_mcangle_it2.35725922
X-RAY DIFFRACTIONr_scbond_it3.92731709
X-RAY DIFFRACTIONr_scangle_it5.9874.51445
X-RAY DIFFRACTIONr_rigid_bond_restr2.29635278
LS refinement shellResolution: 2.5→2.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 138 -
Rwork0.193 2037 -
obs--95.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.3517-1.2084-1.18411.34590.12183.3512-0.0605-0.2756-0.1956-0.12040.11870.12030.2090.1041-0.05820.2239-0.09040.02720.22650.06040.345111.51710.09913.724
22.6797-0.5741-3.14190.22241.06485.6336-0.2506-0.0993-0.2568-0.03220.10310.0374-0.07130.09860.14750.1894-0.02820.00550.30920.0420.3233-2.90815.0422.574
31.6367-0.35731.22850.9946-0.36265.3294-0.4083-0.05580.28620.02410.2728-0.3699-0.2376-0.04250.13550.1272-0.0312-0.01660.1722-0.04170.3937-10.951-8.85723.213
42.85350.04162.39932.3534-0.747.0565-0.03090.43570.18880.01980.0112-0.2260.14830.51060.01970.05570.05220.03780.2553-0.00590.34181.717-13.69631.004
52.91590.5927-3.34950.3206-0.20444.9997-0.19540.1344-0.2576-0.110.083-0.11890.0056-0.06340.11240.22770.04560.05140.2397-0.0080.332339.19251.37331.396
62.77360.9757-1.61620.7777-0.19254.743-0.18430.2934-0.28970.17560.19-0.06770.2627-0.0354-0.00570.16510.07750.02280.2063-0.03540.339824.79146.4640.267
71.018-1.35241.39472.4687-0.56624.3959-0.1553-0.12040.02910.18140.1154-0.0188-0.1952-0.22660.03990.2039-0.0135-0.00770.242-0.00520.387347.15527.45530.834
83.3794-0.73582.05961.04850.49576.1409-0.0345-0.38470.11270.0311-0.07480.23550.0379-0.550.10930.0852-0.05560.00940.26860.03030.383134.19921.80322.592
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A40 - 125
2X-RAY DIFFRACTION2B40 - 132
3X-RAY DIFFRACTION3C38 - 134
4X-RAY DIFFRACTION4D40 - 133
5X-RAY DIFFRACTION5E38 - 131
6X-RAY DIFFRACTION6F40 - 125
7X-RAY DIFFRACTION7G39 - 135
8X-RAY DIFFRACTION8H38 - 133

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