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- PDB-3qxe: Crystal Structure of Co-type Nitrile Hydratase from Pseudomonas p... -

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Basic information

Entry
Database: PDB / ID: 3qxe
TitleCrystal Structure of Co-type Nitrile Hydratase 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, beta subunit / Nitrile Hydratase; Chain A / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / SH3 type barrels. - #50 / Cyclin A; domain 1 / SH3 type barrels. / Roll / Alpha-Beta Complex / Orthogonal Bundle / Mainly Beta ...Nitrile hydratase, beta subunit / Nitrile Hydratase; Chain A / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / 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: 2.104 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 1, 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

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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)195,86420
Polymers194,8928
Non-polymers97212
Water20,5911143
1
A: Co-type Nitrile Hydratase alpha subunit
B: Co-type Nitrile Hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9665
Polymers48,7232
Non-polymers2433
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8290 Å2
ΔGint-43 kcal/mol
Surface area17350 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)48,9665
Polymers48,7232
Non-polymers2433
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8260 Å2
ΔGint-42 kcal/mol
Surface area17350 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)48,9665
Polymers48,7232
Non-polymers2433
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8220 Å2
ΔGint-44 kcal/mol
Surface area17150 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)48,9665
Polymers48,7232
Non-polymers2433
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8260 Å2
ΔGint-43 kcal/mol
Surface area17220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.202, 137.428, 85.384
Angle α, β, γ (deg.)90.00, 92.32, 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 45:47 or resseq...
212chain C and (resseq 4:43 or resseq 45:47 or resseq...
312chain E and (resseq 4:43 or resseq 45:47 or resseq...
412chain G and (resseq 4:43 or resseq 45:47 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: 24054.951 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-3CO / COBALT (III) ION / Cobalt


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1143 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50 mM HEPES, 22% Polyacrylic acid, 20 mM MgCl2, 4% Acetone, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 11, 2007
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→37.6 Å / Num. obs: 108125 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 10.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 2 / Num. unique all: 10093

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Processing

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

1ire


Resolution: 2.104→37.6 Å / SU ML: 0.29 / σ(F): 1.34 / Phase error: 21.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2168 5392 4.99 %
Rwork0.1758 --
obs0.1779 108007 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.993 Å2 / ksol: 0.355 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.0368 Å20 Å2-1.436 Å2
2--1.134 Å20 Å2
3----2.1707 Å2
Refinement stepCycle: LAST / Resolution: 2.104→37.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12973 0 52 1143 14168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113467
X-RAY DIFFRACTIONf_angle_d1.21718385
X-RAY DIFFRACTIONf_dihedral_angle_d15.7964804
X-RAY DIFFRACTIONf_chiral_restr0.0912024
X-RAY DIFFRACTIONf_plane_restr0.0062399
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B1560X-RAY DIFFRACTIONPOSITIONAL
12D1560X-RAY DIFFRACTIONPOSITIONAL0.071
13F1566X-RAY DIFFRACTIONPOSITIONAL0.067
14H1567X-RAY DIFFRACTIONPOSITIONAL0.067
21A1325X-RAY DIFFRACTIONPOSITIONAL
22C1325X-RAY DIFFRACTIONPOSITIONAL0.066
23E1307X-RAY DIFFRACTIONPOSITIONAL0.057
24G1307X-RAY DIFFRACTIONPOSITIONAL0.062
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1042-2.12810.32021550.25832926X-RAY DIFFRACTION85
2.1281-2.15310.28681820.24453200X-RAY DIFFRACTION93
2.1531-2.17940.2831610.24533286X-RAY DIFFRACTION95
2.1794-2.2070.26551870.22273321X-RAY DIFFRACTION96
2.207-2.2360.271730.22953332X-RAY DIFFRACTION96
2.236-2.26660.28151790.22953357X-RAY DIFFRACTION97
2.2666-2.2990.26641710.21393395X-RAY DIFFRACTION98
2.299-2.33330.24841920.20813425X-RAY DIFFRACTION99
2.3333-2.36980.25871880.20613470X-RAY DIFFRACTION100
2.3698-2.40860.26021690.19843458X-RAY DIFFRACTION100
2.4086-2.45020.25351930.19353391X-RAY DIFFRACTION100
2.4502-2.49470.22371850.18763516X-RAY DIFFRACTION100
2.4947-2.54270.23731870.18923411X-RAY DIFFRACTION100
2.5427-2.59460.24231710.17983475X-RAY DIFFRACTION100
2.5946-2.6510.22431690.17853495X-RAY DIFFRACTION100
2.651-2.71260.24391730.17683437X-RAY DIFFRACTION100
2.7126-2.78040.21221920.17273464X-RAY DIFFRACTION100
2.7804-2.85560.22091700.17613488X-RAY DIFFRACTION100
2.8556-2.93960.21352010.17343454X-RAY DIFFRACTION100
2.9396-3.03440.21951990.17323431X-RAY DIFFRACTION100
3.0344-3.14280.22762020.16953464X-RAY DIFFRACTION100
3.1428-3.26860.20431580.17423516X-RAY DIFFRACTION100
3.2686-3.41720.16941520.15883481X-RAY DIFFRACTION100
3.4172-3.59730.18231700.14993477X-RAY DIFFRACTION100
3.5973-3.82250.1961850.15233467X-RAY DIFFRACTION100
3.8225-4.11730.17551870.14663464X-RAY DIFFRACTION100
4.1173-4.5310.1741900.12973466X-RAY DIFFRACTION100
4.531-5.18510.1741800.13883498X-RAY DIFFRACTION100
5.1851-6.52720.18461840.1593506X-RAY DIFFRACTION100
6.5272-37.60880.17691870.15323544X-RAY DIFFRACTION100

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