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- PDB-3qyh: Crystal Structure of Co-type Nitrile Hydratase beta-H71L from Pse... -

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Basic information

Entry
Database: PDB / ID: 3qyh
TitleCrystal Structure of Co-type Nitrile Hydratase beta-H71L 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 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 3, 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 1.4Nov 20, 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)195,02712
Polymers194,7928
Non-polymers2364
Water24,8971382
1
A: Co-type Nitrile Hydratase alpha subunit
B: Co-type Nitrile Hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7573
Polymers48,6982
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7690 Å2
ΔGint-42 kcal/mol
Surface area17370 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)48,7573
Polymers48,6982
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7650 Å2
ΔGint-42 kcal/mol
Surface area17330 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)48,7573
Polymers48,6982
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-41 kcal/mol
Surface area17130 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)48,7573
Polymers48,6982
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7570 Å2
ΔGint-42 kcal/mol
Surface area17230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.978, 137.657, 85.453
Angle α, β, γ (deg.)90.00, 92.45, 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: 24029.961 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


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


Mass: 18.015 Da / Num. of mol.: 1382 / 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: 2.55 Å3/Da / Density % sol: 51.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50 mM HEPES, 22% Polyacrylic acid, 20 mM MgCl2, 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-B / Wavelength: 0.95 Å
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 wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2→45.4 Å / Num. obs: 125221 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 13.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 2 / Num. unique all: 11613

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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→45.4 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 19.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2022 6286 5.02 %
Rwork0.1683 --
obs0.17 125203 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.996 Å2 / ksol: 0.38 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.4622 Å2-0 Å21.8735 Å2
2---3.0956 Å2-0 Å2
3---6.5577 Å2
Refinement stepCycle: LAST / Resolution: 2→45.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12913 0 4 1382 14299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913363
X-RAY DIFFRACTIONf_angle_d1.18818267
X-RAY DIFFRACTIONf_dihedral_angle_d15.7674746
X-RAY DIFFRACTIONf_chiral_restr0.0922028
X-RAY DIFFRACTIONf_plane_restr0.0062385
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B1551X-RAY DIFFRACTIONPOSITIONAL
12D1551X-RAY DIFFRACTIONPOSITIONAL0.071
13F1557X-RAY DIFFRACTIONPOSITIONAL0.063
14H1552X-RAY DIFFRACTIONPOSITIONAL0.066
21A1397X-RAY DIFFRACTIONPOSITIONAL
22C1397X-RAY DIFFRACTIONPOSITIONAL0.064
23E1389X-RAY DIFFRACTIONPOSITIONAL0.055
24G1389X-RAY DIFFRACTIONPOSITIONAL0.057
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9995-2.02230.27141570.22333006X-RAY DIFFRACTION75
2.0223-2.04610.25571780.21893751X-RAY DIFFRACTION92
2.0461-2.0710.27711730.21723805X-RAY DIFFRACTION95
2.071-2.09720.2811840.20123913X-RAY DIFFRACTION97
2.0972-2.12480.242020.18683924X-RAY DIFFRACTION98
2.1248-2.15390.2072340.17943986X-RAY DIFFRACTION99
2.1539-2.18470.21272140.18373960X-RAY DIFFRACTION99
2.1847-2.21730.24542190.17994000X-RAY DIFFRACTION99
2.2173-2.25190.25541930.18744008X-RAY DIFFRACTION99
2.2519-2.28890.22572380.1773946X-RAY DIFFRACTION99
2.2889-2.32830.24062200.17673999X-RAY DIFFRACTION99
2.3283-2.37070.21362090.16894013X-RAY DIFFRACTION99
2.3707-2.41630.22022030.1684015X-RAY DIFFRACTION99
2.4163-2.46560.21772240.16453995X-RAY DIFFRACTION99
2.4656-2.51920.20112000.16394024X-RAY DIFFRACTION100
2.5192-2.57780.21072210.16154010X-RAY DIFFRACTION100
2.5778-2.64220.20441950.16844016X-RAY DIFFRACTION99
2.6422-2.71370.22132190.16463983X-RAY DIFFRACTION100
2.7137-2.79350.19632230.16374024X-RAY DIFFRACTION100
2.7935-2.88370.20242090.1654019X-RAY DIFFRACTION100
2.8837-2.98670.18432150.15924023X-RAY DIFFRACTION100
2.9867-3.10630.19852080.16524040X-RAY DIFFRACTION100
3.1063-3.24760.22312140.16494028X-RAY DIFFRACTION100
3.2476-3.41880.19592070.1594078X-RAY DIFFRACTION100
3.4188-3.63290.17032080.14784018X-RAY DIFFRACTION100
3.6329-3.91320.1612080.1424082X-RAY DIFFRACTION100
3.9132-4.30680.15432380.13434027X-RAY DIFFRACTION100
4.3068-4.92930.15612220.13114041X-RAY DIFFRACTION100
4.9293-6.20790.18482340.16014058X-RAY DIFFRACTION100
6.2079-45.41240.16962170.16184125X-RAY DIFFRACTION100

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