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- PDB-4zge: Double Mutant H80W/H81W of Fe-Type Nitrile Hydratase from Comamon... -

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Basic information

Entry
Database: PDB / ID: 4zge
TitleDouble Mutant H80W/H81W of Fe-Type Nitrile Hydratase from Comamonas testosteroni Ni1
Components
  • Nitrile hydratase alpha subunit
  • Nitrile hydratase beta subunit
KeywordsLYASE / Nitrile Hydratase / Iron / Hydrolysis
Function / homology
Function and homology information


nitrile hydratase / indole-3-acetonitrile nitrile hydratase activity / : / transition metal ion binding
Similarity search - Function
Nitrile hydratase, beta subunit / Nitrile hydratase, beta subunit / Nitrile Hydratase; Chain A / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / Nitrile hydratase beta subunit domain / Nitrile hydratase beta subunit, N-terminal / : / Nitrile hydratase beta subunit, C-terminal / Nitrile hydratase beta subunit, N-terminal / Nitrile hydratase alpha subunit /Thiocyanate hydrolase gamma subunit ...Nitrile hydratase, beta subunit / Nitrile hydratase, beta subunit / Nitrile Hydratase; Chain A / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / Nitrile hydratase beta subunit domain / Nitrile hydratase beta subunit, N-terminal / : / Nitrile hydratase beta subunit, C-terminal / Nitrile hydratase beta subunit, N-terminal / Nitrile hydratase alpha subunit /Thiocyanate hydrolase gamma subunit / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / Nitrile hydratase, alpha chain / Nitrile hydratase alpha /Thiocyanate hydrolase gamma superfamily / SH3 type barrels. - #50 / Electron transport accessory-like domain superfamily / Cyclin A; domain 1 / SH3 type barrels. / Roll / Alpha-Beta Complex / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Nitrile hydratase alpha subunit / Nitrile hydratase subunit beta
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsWu, R. / Martinez, S. / Holz, R. / Liu, D.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2015
Title: Analyzing the catalytic role of active site residues in the Fe-type nitrile hydratase from Comamonas testosteroni Ni1.
Authors: Martinez, S. / Wu, R. / Krzywda, K. / Opalka, V. / Chan, H. / Liu, D. / Holz, R.C.
History
DepositionApr 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Data collection / Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitrile hydratase alpha subunit
B: Nitrile hydratase beta subunit
C: Nitrile hydratase alpha subunit
D: Nitrile hydratase beta subunit
E: Nitrile hydratase alpha subunit
F: Nitrile hydratase beta subunit
G: Nitrile hydratase alpha subunit
H: Nitrile hydratase beta subunit
I: Nitrile hydratase alpha subunit
J: Nitrile hydratase beta subunit
K: Nitrile hydratase alpha subunit
L: Nitrile hydratase beta subunit
M: Nitrile hydratase alpha subunit
N: Nitrile hydratase beta subunit
O: Nitrile hydratase alpha subunit
P: Nitrile hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)365,23824
Polymers364,79116
Non-polymers4478
Water8,017445
1
A: Nitrile hydratase alpha subunit
B: Nitrile hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6553
Polymers45,5992
Non-polymers561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-47 kcal/mol
Surface area18160 Å2
MethodPISA
2
C: Nitrile hydratase alpha subunit
D: Nitrile hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6553
Polymers45,5992
Non-polymers561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-48 kcal/mol
Surface area18200 Å2
MethodPISA
3
E: Nitrile hydratase alpha subunit
F: Nitrile hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6553
Polymers45,5992
Non-polymers561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-49 kcal/mol
Surface area18240 Å2
MethodPISA
4
G: Nitrile hydratase alpha subunit
H: Nitrile hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6553
Polymers45,5992
Non-polymers561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-50 kcal/mol
Surface area18050 Å2
MethodPISA
5
I: Nitrile hydratase alpha subunit
J: Nitrile hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6553
Polymers45,5992
Non-polymers561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-50 kcal/mol
Surface area18300 Å2
MethodPISA
6
K: Nitrile hydratase alpha subunit
L: Nitrile hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6553
Polymers45,5992
Non-polymers561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-47 kcal/mol
Surface area18210 Å2
MethodPISA
7
M: Nitrile hydratase alpha subunit
N: Nitrile hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6553
Polymers45,5992
Non-polymers561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-51 kcal/mol
Surface area18310 Å2
MethodPISA
8
O: Nitrile hydratase alpha subunit
P: Nitrile hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6553
Polymers45,5992
Non-polymers561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-51 kcal/mol
Surface area18150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.680, 111.680, 475.935
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Nitrile hydratase alpha subunit


Mass: 23018.293 Da / Num. of mol.: 8 / Mutation: H80W and H81W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas testosteroni (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: J9PBS0, nitrile hydratase
#2: Protein
Nitrile hydratase beta subunit


Mass: 22580.586 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas testosteroni (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: J9PBS1, nitrile hydratase
#3: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 4.69 Å3/Da / Density % sol: 73.79 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.08 M K2HPO4, 0.49 M NaH2PO4 with 25 or 30% (v/v) glycerol
Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionRedundancy: 3.6 % / Number: 585059 / Rsym value: 0.145 / D res high: 2.8 Å / D res low: 158.645 Å / Num. obs: 163400 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRsym valueRedundancy
8.8567.8410.0460.0463.9
6.268.8510.0530.0533.6
5.116.2610.0750.0753.4
4.435.1110.0930.0933.4
3.964.4310.0950.0953.4
3.613.9610.1330.1333.5
3.353.6110.2050.2053.6
3.133.3510.3350.3353.6
2.953.1310.5230.5233.7
2.82.9510.7240.7243.7
ReflectionResolution: 2.8→67.842 Å / Num. obs: 163400 / % possible obs: 99.9 % / Redundancy: 3.6 % / Rpim(I) all: 0.089 / Rrim(I) all: 0.171 / Rsym value: 0.145 / Net I/av σ(I): 4.733 / Net I/σ(I): 7.3 / Num. measured all: 585059
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.8-2.953.70.724189187238490.4340.7241.9100
2.95-3.133.70.5231.483123225540.3170.5232.6100
3.13-3.353.60.3352.277125212550.2060.3353.8100
3.35-3.613.60.2053.470549197940.1290.2055.7100
3.61-3.963.50.1335.463512181780.0840.1337.9100
3.96-4.433.40.095756255164140.060.09510.5100
4.43-5.113.40.0936.949345145300.0590.09311.999.9
5.11-6.263.40.0758.441890122320.0480.07512.499.9
6.26-8.853.60.05310.63394594350.0330.05315.6100
8.85-67.8423.90.04611.32012851590.0260.04621.199.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SCALA3.3.20data scaling
PHASERphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.15data extraction
Cootmodel building
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→67.842 Å / FOM work R set: 0.7948 / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.229 7707 5.02 %
Rwork0.1811 154832 -
obs0.1835 163011 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.35 Å2 / Biso mean: 48.44 Å2 / Biso min: 22.2 Å2
Refinement stepCycle: final / Resolution: 2.8→67.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25648 0 8 445 26101
Biso mean--50.56 39.08 -
Num. residues----3296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00826336
X-RAY DIFFRACTIONf_angle_d1.16335848
X-RAY DIFFRACTIONf_chiral_restr0.0453928
X-RAY DIFFRACTIONf_plane_restr0.0054624
X-RAY DIFFRACTIONf_dihedral_angle_d13.3339480
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.83180.42042470.347650785325100
2.8318-2.86510.38242750.33352535528100
2.8651-2.90010.36452560.305550965352100
2.9001-2.93680.33392460.310152545500100
2.9368-2.97540.35832650.286250975362100
2.9754-3.01620.33062610.280952605521100
3.0162-3.05930.3062540.273350845338100
3.0593-3.1050.34052800.269352625542100
3.105-3.15350.30842790.256450555334100
3.1535-3.20520.32672870.25351915478100
3.2052-3.26040.27282660.232651455411100
3.2604-3.31970.28892930.221651575450100
3.3197-3.38360.24832930.222252305523100
3.3836-3.45260.26452760.212750865362100
3.4526-3.52770.26272760.202352075483100
3.5277-3.60980.26032960.187251605456100
3.6098-3.70.23042560.172751835439100
3.7-3.80010.21972890.168651245413100
3.8001-3.91190.19922700.157351705440100
3.9119-4.03810.19162910.153651585449100
4.0381-4.18240.21182770.150151495426100
4.1824-4.34990.16942630.13851905453100
4.3499-4.54780.16552800.126751555435100
4.5478-4.78750.18192760.126151665442100
4.7875-5.08740.16382900.124852115501100
5.0874-5.480.17582420.131251425384100
5.48-6.03120.1912810.137551745455100
6.0312-6.90320.19342600.146951975457100
6.9032-8.69440.17152740.126951695443100
8.6944-67.8620.18342800.15945029530998

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