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- PDB-5k8p: Zn2+/Tetrahedral intermediate-bound R289A 5-nitroanthranilate ami... -

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Basic information

Entry
Database: PDB / ID: 5k8p
TitleZn2+/Tetrahedral intermediate-bound R289A 5-nitroanthranilate aminohydrolase
Components5-nitroanthranilic acid aminohydrolase
KeywordsHYDROLASE / Nitroaromatics / deaminase / metalloenzyme
Function / homology
Function and homology information


5-nitroanthranilic acid aminohydrolase / hydrolase activity / metal ion binding
Similarity search - Function
: / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich ...: / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6R8 / 5-nitroanthranilic acid aminohydrolase
Similarity search - Component
Biological speciesBradyrhizobium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKalyoncu, S.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Enzymatic hydrolysis by transition-metal-dependent nucleophilic aromatic substitution.
Authors: Kalyoncu, S. / Heaner, D.P. / Kurt, Z. / Bethel, C.M. / Ukachukwu, C.U. / Chakravarthy, S. / Spain, J.C. / Lieberman, R.L.
History
DepositionMay 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Nov 23, 2016Group: Database references
Revision 1.3Sep 27, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5-nitroanthranilic acid aminohydrolase
B: 5-nitroanthranilic acid aminohydrolase
C: 5-nitroanthranilic acid aminohydrolase
D: 5-nitroanthranilic acid aminohydrolase
E: 5-nitroanthranilic acid aminohydrolase
F: 5-nitroanthranilic acid aminohydrolase
G: 5-nitroanthranilic acid aminohydrolase
H: 5-nitroanthranilic acid aminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)372,97630
Polymers370,5168
Non-polymers2,46122
Water31,3821742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42340 Å2
ΔGint-239 kcal/mol
Surface area101140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.884, 247.634, 247.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-841-

HOH

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Components

#1: Protein
5-nitroanthranilic acid aminohydrolase / 5-nitroanthranilic acid degradation protein A / 5NAA deaminase


Mass: 46314.438 Da / Num. of mol.: 8 / Mutation: R289A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium sp. (bacteria) / Gene: naaA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3)
References: UniProt: D3WZ85, 5-nitroanthranilic acid aminohydrolase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-6R8 / (6~{R})-6-azanyl-3-nitro-6-oxidanyl-cyclohexa-1,3-diene-1-carboxylic acid


Mass: 200.149 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H8N2O5
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 1742 / 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: 3.85 Å3/Da / Density % sol: 68.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium cacodylate pH 6.5, 0.65 M trisodium citrate, 12 mM zinc acetate, 0.22 mM 5-nitroanthranilic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→37.16 Å / Num. obs: 337936 / % possible obs: 98.31 % / Redundancy: 5.7 % / Net I/σ(I): 14.63

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K8O

5k8o


Resolution: 2.2→37.16 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.67
RfactorNum. reflection% reflection
Rfree0.2039 2396 0.71 %
Rwork0.1737 --
obs0.1739 337936 60.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→37.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25900 0 140 1742 27782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01226658
X-RAY DIFFRACTIONf_angle_d1.11836127
X-RAY DIFFRACTIONf_dihedral_angle_d12.9889743
X-RAY DIFFRACTIONf_chiral_restr0.0443863
X-RAY DIFFRACTIONf_plane_restr0.0054768
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2002-2.24510.28881170.227716293X-RAY DIFFRACTION50
2.2451-2.29390.24331180.213516518X-RAY DIFFRACTION51
2.2939-2.34730.22131180.204916591X-RAY DIFFRACTION51
2.3473-2.4060.25581200.201916539X-RAY DIFFRACTION51
2.406-2.4710.21741190.203516582X-RAY DIFFRACTION51
2.471-2.54370.25741190.204616617X-RAY DIFFRACTION51
2.5437-2.62580.2381200.211316621X-RAY DIFFRACTION51
2.6258-2.71960.21471190.206516730X-RAY DIFFRACTION51
2.7196-2.82840.23691200.20616875X-RAY DIFFRACTION52
2.8284-2.95710.2351270.207817428X-RAY DIFFRACTION53
2.9571-3.1130.25661350.211118583X-RAY DIFFRACTION57
3.113-3.30790.21591500.196620715X-RAY DIFFRACTION63
3.3079-3.56310.21621690.183123866X-RAY DIFFRACTION73
3.5631-3.92130.20671690.165124967X-RAY DIFFRACTION76
3.9213-4.48790.17021830.137425190X-RAY DIFFRACTION77
4.4879-5.65110.16581960.137226998X-RAY DIFFRACTION82
5.6511-37.17070.16891970.149328427X-RAY DIFFRACTION87

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