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- PDB-2hyx: Structure of the C-terminal domain of DipZ from Mycobacterium tub... -

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Basic information

Entry
Database: PDB / ID: 2hyx
TitleStructure of the C-terminal domain of DipZ from Mycobacterium tuberculosis
ComponentsProtein dipZ
KeywordsUNKNOWN FUNCTION / Thioredoxin fold / Jelly-roll / Structural Genomics / TB Structural Genomics Consortium / TBSGC / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


cytochrome complex assembly / antioxidant activity / membrane => GO:0016020 / oxidoreductase activity / plasma membrane
Similarity search - Function
DipZ, thioredoxin-like C-terminal domain / Thioredoxin like C-terminal domain / Cytochrome C biogenesis protein, transmembrane domain / Cytochrome C biogenesis protein transmembrane region / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Galactose-binding domain-like / Thioredoxin domain profile. / Thioredoxin domain / Galactose-binding-like domain superfamily ...DipZ, thioredoxin-like C-terminal domain / Thioredoxin like C-terminal domain / Cytochrome C biogenesis protein, transmembrane domain / Cytochrome C biogenesis protein transmembrane region / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Galactose-binding domain-like / Thioredoxin domain profile. / Thioredoxin domain / Galactose-binding-like domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Jelly Rolls / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Protein DipZ / Protein DipZ
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 1.9 Å
AuthorsGoldstone, D. / Baker, E.N. / Metcalf, P. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: To be Published
Title: Structure of the C-terminal domain of DipZ from Mycobacterium tuberculosis
Authors: Goldstone, D. / Baker, E.N. / Metcalf, P.
History
DepositionAug 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein dipZ
B: Protein dipZ
C: Protein dipZ
D: Protein dipZ


Theoretical massNumber of molelcules
Total (without water)152,0704
Polymers152,0704
Non-polymers00
Water16,195899
1
A: Protein dipZ
B: Protein dipZ


Theoretical massNumber of molelcules
Total (without water)76,0352
Polymers76,0352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-20 kcal/mol
Surface area24750 Å2
MethodPISA
2
C: Protein dipZ
D: Protein dipZ


Theoretical massNumber of molelcules
Total (without water)76,0352
Polymers76,0352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-19 kcal/mol
Surface area25080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.070, 117.915, 123.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Protein dipZ


Mass: 38017.434 Da / Num. of mol.: 4 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: dipZ / Plasmid: pProEx-Hta / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pRIL / References: UniProt: Q10801, UniProt: P9WG63*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 899 / 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: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 20% PEG4000, 0.1M Na-Citrate pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 22, 2004
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionAv σ(I) over netI: 10.7 / Number: 468976 / Rmerge(I) obs: 0.11 / Χ2: 1.12 / D res high: 2.4 Å / D res low: 50 Å / Num. obs: 63483 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
5.175099.210.0521.167
4.15.1799.910.0531.017
3.584.199.910.0711.061
3.263.5810010.11.051
3.023.2610010.1441.08
2.853.0210010.231.181
2.72.8510010.3341.168
2.592.710010.4521.18
2.492.5910010.5461.123
2.42.4999.910.6441.125
ReflectionResolution: 1.9→30 Å / Num. all: 126251 / Num. obs: 126251 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.064 / Χ2: 1.107 / Net I/σ(I): 13
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.970.35124890.97199.9
1.97-2.050.234124940.9591100
2.05-2.140.188124881.1351100
2.14-2.250.147125431.1671100
2.25-2.390.112125481.1141100
2.39-2.580.09126011.1411100
2.58-2.840.074126051.0631100
2.84-3.250.059126451.111199.9
3.25-4.090.054127141.407199.7
4.09-300.033131240.989199.8

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Phasing

PhasingMethod: MAD
Phasing dmFOM : 0.64 / FOM acentric: 0.64 / FOM centric: 0.62 / Reflection: 63370 / Reflection acentric: 57914 / Reflection centric: 5456
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.9-50.0910.920.940.8528822273609
4.3-6.90.90.920.79860675591047
3.4-4.30.870.880.77106699691978
3-3.40.750.760.67106999866833
2.6-30.490.490.4318952176701282
2.4-2.60.290.290.261156210855707

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.06phasing
RESOLVE2.05phasing
CNSrefinement
PDB_EXTRACT2data extraction
Blu-Icedata collection
RefinementMethod to determine structure: SAD / Resolution: 1.9→30 Å / FOM work R set: 0.862 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 12262 9.7 %RANDOM
Rwork0.195 ---
all-126251 --
obs-123232 97.6 %-
Solvent computationBsol: 45.036 Å2
Displacement parametersBiso mean: 24.686 Å2
Baniso -1Baniso -2Baniso -3
1--4.023 Å20 Å20 Å2
2--3.279 Å20 Å2
3---0.744 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9919 0 0 899 10818
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.354
X-RAY DIFFRACTIONc_mcbond_it1.1461.5
X-RAY DIFFRACTIONc_scbond_it1.7862
X-RAY DIFFRACTIONc_mcangle_it1.6082
X-RAY DIFFRACTIONc_scangle_it2.5612.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.9-1.910.3211870.30617861973
1.91-1.930.2772330.26420292262
1.93-1.940.2922320.26620562288
1.94-1.950.2932430.25621212364
1.95-1.970.2632120.24321782390
1.97-1.980.2372210.22521332354
1.98-20.2372190.21221882407
2-2.010.2642310.21822022433
2.01-2.030.2482460.21421662412
2.03-2.050.2472260.21621882414
2.05-2.060.2552180.22721382356
2.06-2.080.2492440.21121782422
2.08-2.10.2352570.20421692426
2.1-2.120.2582130.20522652478
2.12-2.140.2512700.21321522422
2.14-2.160.2382120.21522332445
2.16-2.180.2692560.21421982454
2.18-2.20.2322410.19722092450
2.2-2.230.2322520.19922142466
2.23-2.250.2342240.21821662390
2.25-2.280.2342610.20121412402
2.28-2.30.2412390.20322572496
2.3-2.330.2382480.21322172465
2.33-2.360.2372710.21122002471
2.36-2.390.2682570.20922252482
2.39-2.430.2362470.2122162463
2.43-2.460.2382420.20922732515
2.46-2.50.2342630.20622212484
2.5-2.540.2252570.19722182475
2.54-2.580.2482660.20322312497
2.58-2.620.262600.21722522512
2.62-2.670.2472280.21222522480
2.67-2.720.232500.20722092459
2.72-2.780.2592290.21722992528
2.78-2.840.2222750.20722602535
2.84-2.90.2542460.20522722518
2.9-2.980.192460.20622652511
2.98-3.060.2522810.21722532534
3.06-3.150.2272540.20422542508
3.15-3.250.2142460.19722922538
3.25-3.360.2322470.19322752522
3.36-3.50.2352450.19322852530
3.5-3.660.192510.17922832534
3.66-3.850.1942640.17422722536
3.85-4.090.1662530.15923042557
4.09-4.410.1592490.15223112560
4.41-4.850.1672360.14623382574
4.85-5.540.1762630.17423302593
5.54-6.970.2072670.19723492616
6.97-300.1832840.17524472731
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4cis_peptide.param

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