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- PDB-3qz9: Crystal structure of Co-type nitrile hydratase beta-Y215F from Ps... -

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Basic information

Entry
Database: PDB / ID: 3qz9
TitleCrystal structure of Co-type nitrile hydratase beta-Y215F from Pseudomonas putida.
Components
  • Co-type Nitrile Hydratase alpha subunit
  • Co-type Nitrile Hydratase beta subunit
KeywordsLYASE / nitrile hydratase / CO / Cobalt / Cysteine Sulfinic Acid
Function / homology
Function and homology information


Nitrile Hydratase; Chain A / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / Nitrile hydratase, beta subunit / SH3 type barrels. - #50 / Cyclin A; domain 1 / SH3 type barrels. / Roll / Alpha-Beta Complex / Orthogonal Bundle / Mainly Beta ...Nitrile Hydratase; Chain A / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / Nitrile hydratase, beta subunit / SH3 type barrels. - #50 / Cyclin A; domain 1 / SH3 type barrels. / Roll / Alpha-Beta Complex / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBrodkin, H.R. / Novak, W.R.P. / Ringe, D. / Petsko, G.A.
CitationJournal: Biochemistry / Year: 2011
Title: Evidence of the Participation of Remote Residues in the Catalytic Activity of Co-Type Nitrile Hydratase from Pseudomonas putida.
Authors: Brodkin, H.R. / Novak, W.R. / Milne, A.C. / D'Aquino, J.A. / Karabacak, N.M. / Goldberg, I.G. / Agar, J.N. / Payne, M.S. / Petsko, G.A. / Ondrechen, M.J. / Ringe, D.
History
DepositionMar 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Co-type Nitrile Hydratase alpha subunit
B: Co-type Nitrile Hydratase beta subunit
C: Co-type Nitrile Hydratase alpha subunit
D: Co-type Nitrile Hydratase beta subunit
E: Co-type Nitrile Hydratase alpha subunit
F: Co-type Nitrile Hydratase beta subunit
G: Co-type Nitrile Hydratase alpha subunit
H: Co-type Nitrile Hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,43216
Polymers194,8288
Non-polymers6048
Water9,026501
1
A: Co-type Nitrile Hydratase alpha subunit
B: Co-type Nitrile Hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8584
Polymers48,7072
Non-polymers1512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8060 Å2
ΔGint-40 kcal/mol
Surface area17130 Å2
MethodPISA
2
C: Co-type Nitrile Hydratase alpha subunit
D: Co-type Nitrile Hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8584
Polymers48,7072
Non-polymers1512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8060 Å2
ΔGint-40 kcal/mol
Surface area17070 Å2
MethodPISA
3
E: Co-type Nitrile Hydratase alpha subunit
F: Co-type Nitrile Hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8584
Polymers48,7072
Non-polymers1512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7980 Å2
ΔGint-41 kcal/mol
Surface area16920 Å2
MethodPISA
4
G: Co-type Nitrile Hydratase alpha subunit
H: Co-type Nitrile Hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8584
Polymers48,7072
Non-polymers1512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-42 kcal/mol
Surface area16880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.889, 137.203, 86.094
Angle α, β, γ (deg.)90.00, 91.77, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain B and (resseq 1:17 or resseq 22:85 or resseq 103:141 or resseq 143:219 )
211chain D and (resseq 1:17 or resseq 22:85 or resseq 103:141 or resseq 143:219 )
311chain F and (resseq 1:17 or resseq 22:85 or resseq 103:141 or resseq 143:219 )
411chain H and (resseq 1:17 or resseq 22:85 or resseq 103:141 or resseq 143:219 )
112chain A and (resseq 4:43 or resseq 45:52 or resseq...
212chain C and (resseq 4:43 or resseq 45:52 or resseq...
312chain E and (resseq 4:43 or resseq 45:52 or resseq...
412chain G and (resseq 4:43 or resseq 45:52 or resseq...

NCS ensembles :
ID
1
2

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Components

#1: Protein
Co-type Nitrile Hydratase alpha subunit


Mass: 24667.967 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Protein
Co-type Nitrile Hydratase beta subunit


Mass: 24038.951 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-3CO / COBALT (III) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.56 Å3/Da / Density % sol: 51.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50 mM Hepes, 22% polyacrylic acid, 20 mM MgCl, 4% Acetone, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.95 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 8, 2008
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.4→29.8 Å / Num. obs: 74195 / Redundancy: 5.9 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 8.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 2 / Num. unique all: 7160

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IRE

1ire


Resolution: 2.4→29.8 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 21.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2147 3723 5.03 %
Rwork0.185 --
obs0.1865 73983 96.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.947 Å2 / ksol: 0.359 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.4349 Å2-0 Å22.0379 Å2
2---6.5746 Å2-0 Å2
3---8.0096 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12924 0 28 501 13453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713446
X-RAY DIFFRACTIONf_angle_d1.03818371
X-RAY DIFFRACTIONf_dihedral_angle_d14.6654788
X-RAY DIFFRACTIONf_chiral_restr0.0782028
X-RAY DIFFRACTIONf_plane_restr0.0052402
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B1570X-RAY DIFFRACTIONPOSITIONAL
12D1570X-RAY DIFFRACTIONPOSITIONAL0.059
13F1576X-RAY DIFFRACTIONPOSITIONAL0.052
14H1571X-RAY DIFFRACTIONPOSITIONAL0.056
21A1401X-RAY DIFFRACTIONPOSITIONAL
22C1401X-RAY DIFFRACTIONPOSITIONAL0.051
23E1389X-RAY DIFFRACTIONPOSITIONAL0.045
24G1389X-RAY DIFFRACTIONPOSITIONAL0.047
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.377-2.40710.3323620.26081198X-RAY DIFFRACTION44
2.4071-2.43870.29861200.2322519X-RAY DIFFRACTION95
2.4387-2.47210.24431530.22272579X-RAY DIFFRACTION96
2.4721-2.50740.28141310.22452566X-RAY DIFFRACTION96
2.5074-2.54480.27711490.21972606X-RAY DIFFRACTION97
2.5448-2.58460.24981330.21282577X-RAY DIFFRACTION98
2.5846-2.62690.25681240.20482639X-RAY DIFFRACTION98
2.6269-2.67220.27711350.22532631X-RAY DIFFRACTION98
2.6722-2.72070.24721440.21112630X-RAY DIFFRACTION99
2.7207-2.7730.25121280.2082699X-RAY DIFFRACTION99
2.773-2.82960.24491340.20732649X-RAY DIFFRACTION100
2.8296-2.89110.2631450.21392698X-RAY DIFFRACTION100
2.8911-2.95830.26671560.2092658X-RAY DIFFRACTION100
2.9583-3.03220.26421270.20432674X-RAY DIFFRACTION100
3.0322-3.11410.19561520.19892667X-RAY DIFFRACTION100
3.1141-3.20560.25121470.19522662X-RAY DIFFRACTION100
3.2056-3.3090.23561450.18752680X-RAY DIFFRACTION100
3.309-3.42710.19391590.18132688X-RAY DIFFRACTION100
3.4271-3.56410.18061350.15932676X-RAY DIFFRACTION100
3.5641-3.7260.18621570.16942667X-RAY DIFFRACTION100
3.726-3.9220.19631380.1652687X-RAY DIFFRACTION100
3.922-4.16710.16721500.15632663X-RAY DIFFRACTION100
4.1671-4.48790.1661470.14142699X-RAY DIFFRACTION100
4.4879-4.93770.15151410.13732680X-RAY DIFFRACTION100
4.9377-5.64790.19451360.14882703X-RAY DIFFRACTION100
5.6479-7.09990.18011430.16432724X-RAY DIFFRACTION100
7.0999-29.81020.16361320.14632741X-RAY DIFFRACTION99

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