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- PDB-4z7x: MdbA protein, a thiol-disulfide oxidoreductase from Actinomyces oris. -

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Basic information

Entry
Database: PDB / ID: 4z7x
TitleMdbA protein, a thiol-disulfide oxidoreductase from Actinomyces oris.
ComponentsMdbA
KeywordsOXIDOREDUCTASE / thiol-disulfide oxidoreductase / structural genomics / Midwest Center for Structural Genomics / MCSG / PSI-Biology
Function / homologyThioredoxin / Thioredoxin-like fold / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta / Chem-3CX / MdbA
Function and homology information
Biological speciesActinomyces oris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsOSIPIUK, J. / Reardon-Robinson, M.E. / Ton-That, H. / JOACHIMIAK, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE017382 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE025015 United States
CitationJournal: J.Biol.Chem. / Year: 2015
Title: A Disulfide Bond-forming Machine Is Linked to the Sortase-mediated Pilus Assembly Pathway in the Gram-positive Bacterium Actinomyces oris.
Authors: Reardon-Robinson, M.E. / Osipiuk, J. / Chang, C. / Wu, C. / Jooya, N. / Joachimiak, A. / Das, A. / Ton-That, H.
History
DepositionApr 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Sep 20, 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 1.3Dec 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

Downloads & links

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Assembly

Deposited unit
A: MdbA
B: MdbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6954
Polymers51,2212
Non-polymers4752
Water8,125451
1
A: MdbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8482
Polymers25,6101
Non-polymers2371
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MdbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8482
Polymers25,6101
Non-polymers2371
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.880, 66.860, 256.169
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein MdbA


Mass: 25610.330 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinomyces oris (bacteria) / Gene: mdbA, ANA_1994 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0M3KL32*PLUS
#2: Chemical ChemComp-3CX / (2S)-3-(cyclohexylamino)-2-hydroxypropane-1-sulfonic acid


Mass: 237.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H19NO4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / 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: 1.97 Å3/Da / Density % sol: 37.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 37.1 PEG 8000, 0.04 M sodium iodide, 0.15 M CAPSO buffer

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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: Aug 2, 2014
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: 1.55→38.4 Å / Num. all: 59458 / Num. obs: 59458 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.043 / Rrim(I) all: 0.109 / Χ2: 1.863 / Net I/av σ(I): 23.465 / Net I/σ(I): 9.1 / Num. measured all: 371950
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.55-1.584.10.60629380.7140.3320.6960.8598.4
1.58-1.615.10.58328860.8150.2840.6510.89399.9
1.61-1.645.90.54230000.8510.2460.5970.919100
1.64-1.676.50.47728790.8950.2030.5191.02100
1.67-1.716.50.41329720.9250.1750.4491.079100
1.71-1.756.50.37428980.9350.1580.4061.207100
1.75-1.796.50.31329670.950.1320.341.315100
1.79-1.846.50.25529230.9680.1080.2771.505100
1.84-1.896.50.21929420.970.0920.2381.694100
1.89-1.956.50.18930230.9780.080.2061.863100
1.95-2.026.50.15629110.9840.0660.172.031100
2.02-2.16.50.13829430.9880.0580.152.263100
2.1-2.26.50.12229610.990.0510.1332.279100
2.2-2.326.50.11129640.9910.0470.1212.279100
2.32-2.466.50.10129970.9930.0420.112.444100
2.46-2.656.50.09629750.9920.040.1042.384100
2.65-2.926.50.09630400.9930.0410.1042.498100
2.92-3.346.40.08929990.9930.0380.0972.149100
3.34-4.216.30.06530490.9970.0280.072.224100
4.21-506.10.0631910.9970.0260.0663.599.2

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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: 1.55→38.4 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.988 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1799 2954 5 %RANDOM
Rwork0.1239 ---
obs0.1267 56424 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.74 Å2 / Biso mean: 21.32 Å2 / Biso min: 8.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2---0.02 Å20 Å2
3----0.54 Å2
Refinement stepCycle: final / Resolution: 1.55→38.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3175 0 30 451 3656
Biso mean--30.39 33.81 -
Num. residues----419
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.023539
X-RAY DIFFRACTIONr_bond_other_d0.0010.023432
X-RAY DIFFRACTIONr_angle_refined_deg1.611.9754848
X-RAY DIFFRACTIONr_angle_other_deg0.88538024
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4255497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.82126.867150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54915622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.685152
X-RAY DIFFRACTIONr_chiral_restr0.1020.2555
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214062
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02752
X-RAY DIFFRACTIONr_mcbond_it2.981.7881759
X-RAY DIFFRACTIONr_mcbond_other2.9791.7861758
X-RAY DIFFRACTIONr_mcangle_it3.7822.6872213
X-RAY DIFFRACTIONr_rigid_bond_restr3.04836971
X-RAY DIFFRACTIONr_sphericity_free34.1415109
X-RAY DIFFRACTIONr_sphericity_bonded13.78557207
LS refinement shellResolution: 1.546→1.586 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 213 -
Rwork0.181 4028 -
all-4241 -
obs--96.54 %

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