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- PDB-4ese: The crystal structure of azoreductase from Yersinia pestis CO92 i... -

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Basic information

Entry
Database: PDB / ID: 4ese
TitleThe crystal structure of azoreductase from Yersinia pestis CO92 in complex with FMN.
ComponentsFMN-dependent NADH-azoreductase
KeywordsOXIDOREDUCTASE / azoreductase / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID / NIAID / National Institute of Allergy and Infectious Diseases
Function / homology
Function and homology information


Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor / FMN-dependent NADH-azoreductase / 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
FLAVIN MONONUCLEOTIDE / IMIDAZOLE / FMN-dependent NADH:quinone oxidoreductase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsTan, K. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: The crystal structure of acyl carrier protein phosphodiesterase from Yersinia pestis CO92 in complex with FMN.
Authors: Tan, K. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionApr 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FMN-dependent NADH-azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9677
Polymers21,8901
Non-polymers2,0776
Water3,477193
1
A: FMN-dependent NADH-azoreductase
hetero molecules

A: FMN-dependent NADH-azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,93414
Polymers43,7802
Non-polymers4,15412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area7090 Å2
ΔGint-32 kcal/mol
Surface area18960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.825, 120.388, 60.074
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-306-

IMD

21A-556-

HOH

31A-587-

HOH

DetailsExperimental unknown. It is predicted that the Chain A and its symmetry-related molecule by the operator ( -x,y,-z+1/2) may form a dimer.

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 21890.006 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: azoR, y2010, YPO2323, 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

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Non-polymers , 5 types, 199 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.14 Å3/Da / Density % sol: 42.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 15% (w/v) PEG1500, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2012 / Details: mirror
RadiationMonochromator: Si 11 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.45→26 Å / Num. all: 33841 / Num. obs: 33841 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 38.5
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1669 / % possible all: 99.6

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1T5B

1t5b


Resolution: 1.45→25.403 Å / SU ML: 0.34 / σ(F): 1.34 / Phase error: 20.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1714 5.07 %random
Rwork0.1739 ---
all0.1753 33809 --
obs0.1753 33809 99.8 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.357 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.0295 Å20 Å20 Å2
2--1.6698 Å2-0 Å2
3---5.3597 Å2
Refinement stepCycle: LAST / Resolution: 1.45→25.403 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1463 0 125 193 1781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061645
X-RAY DIFFRACTIONf_angle_d1.0572241
X-RAY DIFFRACTIONf_dihedral_angle_d14.351603
X-RAY DIFFRACTIONf_chiral_restr0.073256
X-RAY DIFFRACTIONf_plane_restr0.005271
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4478-1.49040.30231380.27842636X-RAY DIFFRACTION99
1.4904-1.53850.31721400.24872626X-RAY DIFFRACTION100
1.5385-1.59350.23951430.21472646X-RAY DIFFRACTION100
1.5935-1.65730.22241500.19222627X-RAY DIFFRACTION100
1.6573-1.73270.23271460.18592655X-RAY DIFFRACTION100
1.7327-1.82410.22981420.18062670X-RAY DIFFRACTION100
1.8241-1.93830.22241290.17492676X-RAY DIFFRACTION100
1.9383-2.08790.21991230.17052681X-RAY DIFFRACTION100
2.0879-2.29790.1881520.16532660X-RAY DIFFRACTION100
2.2979-2.63010.1871480.17012706X-RAY DIFFRACTION100
2.6301-3.31250.20921440.17432722X-RAY DIFFRACTION100
3.3125-25.40640.171590.15972790X-RAY DIFFRACTION99
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)
13.05410.0661-0.57732.17180.44891.22290.04080.29440.0181-0.21330.01830.2022-0.0367-0.3523-0.17470.1206-0.0042-0.03850.1302-0.00730.1304-11.8115-18.32730.4467
22.1677-0.51650.61693.0519-2.87752.7731-0.21230.06670.1312-0.07190.14160.085-0.0313-0.87720.09540.16910.0118-0.05290.2386-0.01160.2371-18.3312-14.294-2.0254
33.1283-1.23593.37992.0813-1.72984.05250.22010.3134-0.1747-0.2952-0.020.21090.35310.2488-0.20490.1706-0.00970.00730.1665-0.03050.12-6.1271-22.2097-0.1503
41.6494-3.3517-0.13027.20361.36022.98720.06970.18340.2395-0.47420.043-1.13350.05710.3669-0.13410.19690.01320.04930.2292-0.02520.295515.709-27.61146.7678
52.7178-3.63723.07276.242-5.01734.11310.12650.0811-0.103-0.4134-0.0610.08510.38870.0374-0.04450.20710.01880.01640.1649-0.02550.12565.6776-26.1847-0.1022
60.81660.21160.29730.6707-0.32821.4646-0.0158-0.01180.00610.01610.014-0.0024-0.0668-0.02450.0030.1624-0.006-0.00120.1350.00010.1275-3.7251-15.47987.3844
73.92653.9047-0.60363.9177-0.32645.0844-0.14220.20970.2618-0.26410.0674-0.6119-0.39560.59740.11010.1691-0.02310.01940.21050.00620.277514.8801-10.1696-0.9046
86.5955-1.3507-0.06522.2987-0.12431.3680.07520.60750.3842-0.1373-0.06470.0844-0.0525-0.0453-0.03680.1745-0.0081-0.0160.19190.00450.1848-3.146-9.1675-2.9402
94.84010.93281.97735.339-1.16276.165-0.1169-0.28210.3880.3805-0.00580.5638-0.3907-0.41470.08520.20910.02180.01310.15-0.00640.2311-2.7209-5.49678.6387
105.8898-0.7597-1.64551.87930.46172.68560.16510.18840.2793-0.0206-0.11870.1843-0.2493-0.2194-0.05250.1791-0.0178-0.00720.14090.00350.2235-4.4427-5.03890.3217
117.6781.93614.31711.32612.12225.50250.3151-0.78690.74830.44730.2611-0.43990.00990.3625-0.53590.30650.095-0.01230.4952-0.19840.3485-26.1747-10.98388.3416
123.99323.6889-5.1245.7719-3.36627.4295-0.08760.41640.8671-0.04430.2070.298-0.2498-0.4549-0.06180.16850.0413-0.05180.2794-0.0210.3579-21.9616-6.6825-1.6463
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 0:16)A0 - 16
2X-RAY DIFFRACTION2chain 'A' and (resseq 17:32)A17 - 32
3X-RAY DIFFRACTION3chain 'A' and (resseq 33:52)A33 - 52
4X-RAY DIFFRACTION4chain 'A' and (resseq 53:67)A53 - 67
5X-RAY DIFFRACTION5chain 'A' and (resseq 68:86)A68 - 86
6X-RAY DIFFRACTION6chain 'A' and (resseq 87:112)A87 - 112
7X-RAY DIFFRACTION7chain 'A' and (resseq 113:128)A113 - 128
8X-RAY DIFFRACTION8chain 'A' and (resseq 129:139)A129 - 139
9X-RAY DIFFRACTION9chain 'A' and (resseq 140:163)A140 - 163
10X-RAY DIFFRACTION10chain 'A' and (resseq 164:173)A164 - 173
11X-RAY DIFFRACTION11chain 'A' and (resseq 174:185)A174 - 185
12X-RAY DIFFRACTION12chain 'A' and (resseq 186:200)A186 - 200

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