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- PDB-5c00: MdbA protein, a thiol-disulfide oxidoreductase from Corynebacteri... -

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Basic information

Entry
Database: PDB / ID: 5c00
TitleMdbA protein, a thiol-disulfide oxidoreductase from Corynebacterium diphtheriae
ComponentsMdbA proteinMurray–Darling Basin Authority
KeywordsOXIDOREDUCTASE / MdbA / dip1880 / thiol-disulfide oxidoreductase / Structural Genomics / Midwest Center for Structural Genomics / MCSG / PSI-Biology
Function / homologyThioredoxin / Thioredoxin-like fold / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / membrane => GO:0016020 / 3-Layer(aba) Sandwich / Alpha Beta / Putative exported protein
Function and homology information
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.77 Å
AuthorsOSIPIUK, J. / REARDON-ROBINSON, M.E. / TON-THAT, H. / JOACHIMIAK, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE025015 United States
CitationJournal: Mol.Microbiol. / Year: 2015
Title: A thiol-disulfide oxidoreductase of the Gram-positive pathogen Corynebacterium diphtheriae is essential for viability, pilus assembly, toxin production and virulence.
Authors: Reardon-Robinson, M.E. / Osipiuk, J. / Jooya, N. / Chang, C. / Joachimiak, A. / Das, A. / Ton-That, H.
History
DepositionJun 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MdbA protein
B: MdbA protein
C: MdbA protein
D: MdbA protein


Theoretical massNumber of molelcules
Total (without water)91,1874
Polymers91,1874
Non-polymers00
Water7,170398
1
A: MdbA protein


Theoretical massNumber of molelcules
Total (without water)22,7971
Polymers22,7971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MdbA protein


Theoretical massNumber of molelcules
Total (without water)22,7971
Polymers22,7971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: MdbA protein


Theoretical massNumber of molelcules
Total (without water)22,7971
Polymers22,7971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: MdbA protein


Theoretical massNumber of molelcules
Total (without water)22,7971
Polymers22,7971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.532, 76.621, 72.586
Angle α, β, γ (deg.)90.000, 90.170, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
MdbA protein / Murray–Darling Basin Authority


Mass: 22796.859 Da / Num. of mol.: 4 / Fragment: UNP residues 40-244
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis) (bacteria)
Strain: ATCC 700971 / NCTC 13129 / Biotype gravis / Gene: DIP1880 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6NFK7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 1.92 Å3/Da / Density % sol: 36.05 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 4.3 % w/v PEG 2000, 50 mM Tris pH 8.0, 28.6 % v/v PEG 550 MME, microseeding

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2013
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. all: 65737 / Num. obs: 65737 / % possible obs: 99.9 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.039 / Rrim(I) all: 0.088 / Χ2: 2.007 / Net I/av σ(I): 29.901 / Net I/σ(I): 10.5 / Num. measured all: 318208
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.77-1.840.6172.0232430.7520.3510.7130.75699.4
1.8-1.834.40.5232640.8540.2790.5920.785100
1.83-1.874.90.48933120.8840.2450.5480.848100
1.87-1.9150.39632670.9450.1960.4430.847100
1.91-1.9550.33332420.9380.1640.3720.905100
1.95-1.9950.27132980.9630.1350.3040.967100
1.99-2.0450.22432770.9720.1110.251.037100
2.04-2.150.18332680.9790.090.2051.134100
2.1-2.1650.15432920.9850.0750.1721.285100
2.16-2.2350.13732590.9860.0680.1531.441100
2.23-2.3150.11832880.9890.0580.1321.599100
2.31-2.450.10932760.9910.0540.1221.677100
2.4-2.5150.09933010.9920.0490.111.81100
2.51-2.6450.09132900.9930.0450.1012.158100
2.64-2.8150.08432880.9930.0410.0942.486100
2.81-3.034.90.07632780.9940.0380.0853.017100
3.03-3.334.80.06933030.9950.0350.0783.75199.9
3.33-3.814.70.06233220.9950.0320.0694.36799.9
3.81-4.84.70.05133070.9970.0260.0584.12599.9
4.8-504.70.04933620.9970.0250.0555.07899

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.77→34 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.996 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2098 3299 5 %RANDOM
Rwork0.1619 ---
obs0.1642 62417 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.53 Å2 / Biso mean: 33.462 Å2 / Biso min: 14.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å2-0 Å2-0.52 Å2
2--2.4 Å20 Å2
3----1.54 Å2
Refinement stepCycle: final / Resolution: 1.77→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6109 0 0 399 6508
Biso mean---35.08 -
Num. residues----792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.026508
X-RAY DIFFRACTIONr_bond_other_d0.0010.026086
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.9518830
X-RAY DIFFRACTIONr_angle_other_deg0.812314158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4655877
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.17226.055327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.618151158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2471524
X-RAY DIFFRACTIONr_chiral_restr0.0930.2940
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027630
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021440
X-RAY DIFFRACTIONr_mcbond_it1.3731.9253256
X-RAY DIFFRACTIONr_mcbond_other1.3731.9253255
X-RAY DIFFRACTIONr_mcangle_it2.0872.8784086
LS refinement shellResolution: 1.769→1.815 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 244 -
Rwork0.269 4531 -
all-4775 -
obs--98.72 %
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)
11.1542-0.46030.15910.280.020.8174-0.0153-0.015-0.10.02580.01690.0266-0.0396-0.0305-0.00160.0206-0.00080.00350.00670.00310.088247.489531.724656.1333
20.85370.0512-0.06310.2191-0.13750.8036-0.02660.0835-0.0115-0.01830.0026-0.05390.0267-0.05640.0240.0328-0.00320.0230.012-0.00180.082416.828546.913548.0067
30.81770.50320.16821.8014-1.09794.3216-0.07060.19420.2203-0.14510.07220.1689-0.42180.4172-0.00160.0943-0.0582-0.01040.12240.01860.100842.168745.532322.1542
41.3821-0.00740.37212.03340.00094.12760.0472-0.2815-0.28190.4791-0.03180.09640.5645-0.2316-0.01540.2281-0.0316-0.00230.12080.04070.141312.043133.65419.4593
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 244
2X-RAY DIFFRACTION2B43 - 244
3X-RAY DIFFRACTION3C47 - 243
4X-RAY DIFFRACTION4D49 - 239

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