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- PDB-4zgd: Mutant R157A of Fe-Type Nitrile Hydratase from Comamonas testoste... -

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Basic information

Entry
Database: PDB / ID: 4zgd
TitleMutant R157A 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 / Resolution: 2.25 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)363,78024
Polymers363,33316
Non-polymers4478
Water53,9552995
1
A: Nitrile hydratase alpha subunit
B: Nitrile hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4723
Polymers45,4172
Non-polymers561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-51 kcal/mol
Surface area18150 Å2
MethodPISA
2
C: Nitrile hydratase alpha subunit
D: Nitrile hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4723
Polymers45,4172
Non-polymers561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-46 kcal/mol
Surface area17940 Å2
MethodPISA
3
E: Nitrile hydratase alpha subunit
F: Nitrile hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4723
Polymers45,4172
Non-polymers561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-49 kcal/mol
Surface area18000 Å2
MethodPISA
4
G: Nitrile hydratase alpha subunit
H: Nitrile hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4723
Polymers45,4172
Non-polymers561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-49 kcal/mol
Surface area18030 Å2
MethodPISA
5
I: Nitrile hydratase alpha subunit
J: Nitrile hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4723
Polymers45,4172
Non-polymers561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-52 kcal/mol
Surface area18060 Å2
MethodPISA
6
K: Nitrile hydratase alpha subunit
L: Nitrile hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4723
Polymers45,4172
Non-polymers561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-49 kcal/mol
Surface area18040 Å2
MethodPISA
7
M: Nitrile hydratase alpha subunit
N: Nitrile hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4723
Polymers45,4172
Non-polymers561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-51 kcal/mol
Surface area18140 Å2
MethodPISA
8
O: Nitrile hydratase alpha subunit
P: Nitrile hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4723
Polymers45,4172
Non-polymers561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-50 kcal/mol
Surface area17970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.590, 111.590, 474.604
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: 22836.053 Da / Num. of mol.: 8 / Mutation: R157A
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.: 2995 / 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: 73.78 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: Hanging Drop with reservoir solution as the following: 1.08 M K2HPO4, 0.49 M NaH2PO4 with 25 or 30% (v/v) glycerol
PH range: 7 / 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
ReflectionResolution: 2.25→50.491 Å / Num. obs: 313740 / % possible obs: 100 % / Redundancy: 3.8 % / Rpim(I) all: 0.093 / Rrim(I) all: 0.182 / Rsym value: 0.156 / Net I/av σ(I): 4.347 / Net I/σ(I): 6.9 / Num. measured all: 1185275
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
2.25-2.373.70.7241171800458880.4320.7242.1100
2.37-2.523.80.5791.3162598433420.3450.5792.6100
2.52-2.693.80.4321.7153136406720.2570.4323.3100
2.69-2.93.80.2982.5143053379460.1780.2984.4100
2.9-3.183.80.23.6132172349630.1190.26.2100
3.18-3.563.80.1265.4119854315670.0750.1269.4100
3.56-4.113.80.0867.6105713277880.0510.08613100
4.11-5.033.80.079.189586234990.0420.0715.3100
5.03-7.123.80.0649.769330181280.0380.06414.1100
7.12-50.5593.80.052103803399470.0310.05217.299.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.20data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementResolution: 2.25→50.491 Å / FOM work R set: 0.8585 / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2032 15125 5.05 %
Rwork0.1725 297626 -
obs0.174 313458 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.98 Å2 / Biso mean: 31.78 Å2 / Biso min: 12.87 Å2
Refinement stepCycle: final / Resolution: 2.25→50.491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25536 0 8 2995 28539
Biso mean--32.74 37.7 -
Num. residues----3296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00726222
X-RAY DIFFRACTIONf_angle_d1.07535686
X-RAY DIFFRACTIONf_chiral_restr0.0433930
X-RAY DIFFRACTIONf_plane_restr0.0054620
X-RAY DIFFRACTIONf_dihedral_angle_d13.0969450
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 (%)
2.25-2.27560.29815320.27231002710559100
2.2756-2.30240.28485230.2583981710340100
2.3024-2.33040.28375590.2613997010529100
2.3304-2.35990.29565230.2537990210425100
2.3599-2.3910.27685290.2464981910348100
2.391-2.42380.26075110.24081005710568100
2.4238-2.45840.26075560.2353982110377100
2.4584-2.49510.28035200.2339989710417100
2.4951-2.53410.285220.22521004310565100
2.5341-2.57560.2745390.222980210341100
2.5756-2.620.26265220.2182991010432100
2.62-2.66770.2555360.2075994910485100
2.6677-2.7190.24065440.2031996710511100
2.719-2.77450.2345150.1994986810383100
2.7745-2.83480.23855050.1972994810453100
2.8348-2.90070.22764990.1912990110400100
2.9007-2.97320.22695580.1842994910507100
2.9732-3.05360.24765220.191989310415100
3.0536-3.14350.22155130.1803996210475100
3.1435-3.24490.19275310.1676994010471100
3.2449-3.36090.20785300.1642993710467100
3.3609-3.49540.19155480.1615991610464100
3.4954-3.65440.17515060.1471992810434100
3.6544-3.8470.16995040.1418998810492100
3.847-4.0880.15595110.1274989410405100
4.088-4.40340.15145120.1229995210464100
4.4034-4.84630.13335450.117996210507100
4.8463-5.54680.15235600.13986410424100
5.5468-6.98540.16995340.1478992510459100
6.9854-50.50370.15885230.14498181034199

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