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- PDB-3wuy: Crystal structure of Nit6803 -

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Basic information

Entry
Database: PDB / ID: 3wuy
TitleCrystal structure of Nit6803
ComponentsNitrilase
KeywordsHYDROLASE / Nitrilase
Function / homology
Function and homology information


Nitrilase-related, sll0784 / Nitrilases / cyanide hydratase active site signature. / Nitrilase/Cyanide hydratase / Nitrilase/cyanide hydratase, conserved site / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Phosphatidylinositol-specific phospholipase X-box domain profile. / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase ...Nitrilase-related, sll0784 / Nitrilases / cyanide hydratase active site signature. / Nitrilase/Cyanide hydratase / Nitrilase/cyanide hydratase, conserved site / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Phosphatidylinositol-specific phospholipase X-box domain profile. / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSynechocystis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.1 Å
AuthorsYuan, Y.A. / Yin, B. / Wang, C.
CitationJournal: J.Struct.Biol. / Year: 2014
Title: Structural insights into enzymatic activity and substrate specificity determination by a single amino acid in nitrilase from Syechocystis sp. PCC6803
Authors: Zhang, L. / Yin, B. / Wang, C. / Jiang, S. / Wang, H. / Yuan, Y.A. / Wei, D.
History
DepositionMay 9, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitrilase
B: Nitrilase


Theoretical massNumber of molelcules
Total (without water)76,6142
Polymers76,6142
Non-polymers00
Water724
1
A: Nitrilase


Theoretical massNumber of molelcules
Total (without water)38,3071
Polymers38,3071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nitrilase


Theoretical massNumber of molelcules
Total (without water)38,3071
Polymers38,3071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-5 kcal/mol
Surface area23240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.545, 113.545, 161.009
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 6 - 290 / Label seq-ID: 9 - 293

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Nitrilase


Mass: 38306.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis (bacteria) / Strain: PCC 6803 / Gene: merR / Production host: Escherichia coli (E. coli) / References: UniProt: Q55949
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.91 Å3/Da / Density % sol: 68.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Sodium Cacodylate, PEG4K, MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 20, 2012
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 20270 / Num. obs: 20231 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.1→3.18 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD
Starting model: Structure determined by MAD and refinement using the native data.

Resolution: 3.1→49.21 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 24.022 / SU ML: 0.199 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.69 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19237 1096 5.1 %RANDOM
Rwork0.16419 ---
all0.166 20270 --
obs0.16565 20231 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.374 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20.82 Å2-0 Å2
2--0.82 Å2-0 Å2
3----2.66 Å2
Refinement stepCycle: LAST / Resolution: 3.1→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4429 0 0 4 4433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0194523
X-RAY DIFFRACTIONr_bond_other_d0.0050.024370
X-RAY DIFFRACTIONr_angle_refined_deg1.9911.9536125
X-RAY DIFFRACTIONr_angle_other_deg1.062310047
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.635572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.87724.271192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.54915775
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4091522
X-RAY DIFFRACTIONr_chiral_restr0.1010.2688
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215126
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021024
Refine LS restraints NCS

Ens-ID: 1 / Number: 17181 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.099→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 84 -
Rwork0.212 1470 -
obs--99.04 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.11320.0713-0.11462.36610.28852.2731-0.06310.1536-0.0885-0.185-0.05680.0295-0.2701-0.11080.120.06440.01740.0010.0156-0.02670.1493-2.704-47.2175-25.2783
23.517-0.6644-0.40582.1792-0.18322.4135-0.0323-0.2626-0.13060.2357-0.01110.0264-0.14950.19250.04330.13470.030.00580.05420.04280.1794-9.3946-46.633711.2437
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 291
2X-RAY DIFFRACTION2B6 - 292

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