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- PDB-5jro: The crystal structure of azoreductase from Yersinia pestis CO92 i... -

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Basic information

Entry
Database: PDB / ID: 5jro
TitleThe crystal structure of azoreductase from Yersinia pestis CO92 in its Apo form
ComponentsFMN-dependent NADH-azoreductase
KeywordsOXIDOREDUCTASE / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


FMN-dependent NADH-azoreductase / Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor / oxidoreductase activity, acting on NAD(P)H as acceptor / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / FMN binding / electron transfer activity
Similarity search - Function
NADH:quinone oxidoreductase, FMN-dependent / : / Flavodoxin-like fold / Flavodoxin-like fold / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FMN-dependent NADH:quinone oxidoreductase
Similarity search - Component
Biological speciesYersinia pestis CO92 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsTan, K. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
CitationJournal: To Be Published
Title: The crystal structure of azoreductase from Yersinia pestis CO92 in its Apo form
Authors: Tan, K. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionMay 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 4, 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
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: FMN-dependent NADH-azoreductase
B: FMN-dependent NADH-azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9644
Polymers43,7802
Non-polymers1842
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-20 kcal/mol
Surface area16730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.257, 45.135, 72.699
Angle α, β, γ (deg.)90.00, 112.84, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein FMN-dependent NADH-azoreductase / Azo-dye reductase / FMN-dependent NADH-azo compound oxidoreductase


Mass: 21890.006 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis CO92 (bacteria) / Strain: CO92 / Gene: azoR, YPO2323, y2010, YP_2110 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic
References: UniProt: Q8ZE60, Oxidoreductases; Acting on other nitrogenous compounds as donors
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.15 Å3/Da / Density % sol: 42.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 0.1M CHES:NaOH, 30% (w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 28, 2014 / Details: Mirror
RadiationMonochromator: Si 111 Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.54→33.5 Å / Num. obs: 12240 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 25.74
Reflection shellResolution: 2.54→2.58 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 2.35 / % possible all: 81.3

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Processing

Software
NameVersionClassification
PHENIX(dev-2386_1692: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 4ESE
Resolution: 2.54→33.5 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26
RfactorNum. reflection% reflectionSelection details
Rfree0.2489 529 4.85 %random
Rwork0.1997 ---
obs0.202 10911 86.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.54→33.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2753 0 12 20 2785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032804
X-RAY DIFFRACTIONf_angle_d0.5113811
X-RAY DIFFRACTIONf_dihedral_angle_d15.1941685
X-RAY DIFFRACTIONf_chiral_restr0.041468
X-RAY DIFFRACTIONf_plane_restr0.004486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.7850.31971030.27611813X-RAY DIFFRACTION62
2.785-3.18770.29041140.24982532X-RAY DIFFRACTION85
3.1877-4.01510.28011520.19792987X-RAY DIFFRACTION100
4.0151-33.50.20041600.16773050X-RAY DIFFRACTION99
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)
19.72170.6865-5.47325.3769-1.57228.9143-0.6360.4646-1.0007-0.63420.2661-0.93230.8179-0.76090.3890.4225-0.019-0.0540.2743-0.09610.374433.4312-35.5325-16.8249
23.09641.16070.29984.03072.29053.2533-0.108-0.0965-0.35-0.0135-0.1642-0.41150.3989-0.38620.43331.03670.0439-0.04140.2198-0.1750.539634.7872-42.3407-20.6694
32.2621-1.1895-0.52654.7483.72423.0637-0.12760.1142-0.1651-0.60270.4585-0.8290.10940.5933-0.19670.52130.16190.18440.4213-0.0240.482141.8183-35.9413-18.327
43.80290.2816-1.48113.65070.36293.4419-0.0342-0.53720.53360.28290.3856-0.73860.01510.24580.09420.1336-0.0820.04550.4087-0.07650.222328.4035-24.1563-7.4328
57.0404-2.45994.982.375-1.97653.8076-0.2546-0.12462.2093-0.5414-0.1223-0.5545-2.22941.05190.37720.6285-0.13410.16340.4229-0.04190.73632.1732-7.8483-6.4721
61.9697-0.03540.28241.35610.46211.28530.2576-0.2357-0.1294-0.34240.1325-0.1947-0.12920.1873-0.22120.173-0.03830.12280.3034-0.05690.137131.0617-23.3423-14.5509
73.0771-0.53452.11880.1450.05784.9458-0.07550.36870.2858-1.23170.0354-0.6132-1.06850.2787-0.06310.655-0.08540.19410.3751-0.00380.30335.9481-11.8965-26.2932
81.2328-1.5201-1.41014.3311-0.21073.18180.16930.5282-0.5944-0.2393-0.15570.60490.1037-0.9390.56760.6269-0.07820.04520.6018-0.15990.316722.1168-32.1799-27.2439
95.121-1.07370.51614.99190.69644.7232-0.03220.4507-0.6077-1.04010.05010.29930.3783-0.18140.03850.5433-0.0323-0.00510.292-0.00110.234126.9146-27.3561-27.584
107.5702-1.16824.43259.005-0.12978.7116-0.47850.8502-0.5045-0.7192-0.16680.76150.00920.13130.55510.86460.0420.08980.4003-0.13660.403931.6293-43.5733-29.7787
117.5798-3.43581.40814.1873-0.84312.9355-0.06180.0810.44790.092-0.05270.5524-0.6120.11430.11620.3083-0.014-0.03920.21040.00190.33366.291-9.4488-7.9362
123.9478-0.4086-1.81232.5955-0.99343.56370.1625-0.2418-0.16410.08210.01340.4323-0.07270.035-0.08980.1457-0.0929-0.08350.1836-0.05860.195510.4913-25.2835-6.2798
131.6271-0.66350.32363.9922-0.20212.5255-0.04150.20980.204-0.65470.01830.1783-0.1177-0.0209-0.00290.3109-0.0303-0.13010.23840.03520.31995.7741-19.4813-18.473
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 32 )
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 42 )
4X-RAY DIFFRACTION4chain 'A' and (resid 43 through 52 )
5X-RAY DIFFRACTION5chain 'A' and (resid 53 through 67 )
6X-RAY DIFFRACTION6chain 'A' and (resid 68 through 112 )
7X-RAY DIFFRACTION7chain 'A' and (resid 113 through 133 )
8X-RAY DIFFRACTION8chain 'A' and (resid 134 through 152 )
9X-RAY DIFFRACTION9chain 'A' and (resid 153 through 189 )
10X-RAY DIFFRACTION10chain 'A' and (resid 190 through 201 )
11X-RAY DIFFRACTION11chain 'B' and (resid 0 through 52 )
12X-RAY DIFFRACTION12chain 'B' and (resid 53 through 102 )
13X-RAY DIFFRACTION13chain 'B' and (resid 103 through 201 )

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