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- PDB-6nbo: Crystal structure of N-isopropylammelide isopropylaminohydrolase ... -

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Basic information

Entry
Database: PDB / ID: 6nbo
TitleCrystal structure of N-isopropylammelide isopropylaminohydrolase from Burkholderia multivorans ATCC 17616
ComponentsN-isopropylammelide isopropylaminohydrolase
KeywordsHYDROLASE / SSGCID / Burkholderia multivorans / N-isopropylammelide isopropylaminohydrolase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


N-isopropylammelide isopropylaminohydrolase / N-isopropylammelide isopropylaminohydrolase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines / metal ion binding
Similarity search - Function
: / Amidohydrolase 3 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Metal-dependent hydrolase
Similarity search - Domain/homology
N-isopropylammelide isopropylaminohydrolase
Similarity search - Component
Biological speciesBurkholderia multivorans ATCC 17616 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of N-isopropylammelide isopropylaminohydrolase from Burkholderia multivorans ATCC 17616
Authors: Conrady, D.G. / Mayclin, S.J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionDec 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-isopropylammelide isopropylaminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,34313
Polymers42,7511
Non-polymers59212
Water6,774376
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.260, 100.350, 142.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-577-

HOH

21A-630-

HOH

31A-844-

HOH

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Components

#1: Protein N-isopropylammelide isopropylaminohydrolase


Mass: 42750.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia multivorans ATCC 17616 (bacteria)
Strain: ATCC 17616 / 249 / Gene: atzC, BMULJ_05300 / Plasmid: BumuA.00109.b.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0H3KPJ4, N-isopropylammelide isopropylaminohydrolase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 3.82 Å3/Da / Density % sol: 67.84 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: BumuA.00109.b.B1.PS37886 at 23.1mg/ml, mixed 1:1 with JCSG+g12: 3M NacL, 0.1M Bis-Tris pH5.5, cryo protected with 20% EG. Crystal id 272543g12, nmv9-9.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.95→42.899 Å / Num. obs: 46373 / % possible obs: 100 % / Redundancy: 7.369 % / Biso Wilson estimate: 35.063 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.062 / Χ2: 1.006 / Net I/σ(I): 21.42 / Num. measured all: 341726
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.95-27.5070.5183.8133960.9070.556100
2-2.067.5030.3855.1532990.9440.413100
2.06-2.127.5230.2956.6332250.970.317100
2.12-2.187.5150.2368.1731110.9790.253100
2.18-2.257.5130.1949.9830200.9830.208100
2.25-2.337.5220.16111.8729690.9890.173100
2.33-2.427.50.13214.328260.9920.142100
2.42-2.527.5070.10817.0727300.9950.116100
2.52-2.637.4790.08920.2926180.9970.096100
2.63-2.767.4520.07623.3425160.9970.081100
2.76-2.917.3640.06626.523910.9980.071100
2.91-3.087.3270.05631.0122640.9980.06100
3.08-3.37.2130.04835.4521410.9980.052100
3.3-3.567.130.04140.4419920.9990.044100
3.56-3.97.0710.03843.1118550.9990.041100
3.9-4.366.9990.03445.8916660.9990.037100
4.36-5.037.060.03147.5614890.9990.034100
5.03-6.177.0890.03146.7312770.9990.033100
6.17-8.726.9390.02647.5310010.9990.029100
8.72-42.8996.2540.02547.215870.9990.02798.2

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Processing

Software
NameVersionClassification
PHENIXdev_3339refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CQB

4cqb


Resolution: 1.95→42.899 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1783 2000 4.31 %
Rwork0.1573 --
obs0.1582 46367 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→42.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2857 0 24 376 3257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062987
X-RAY DIFFRACTIONf_angle_d0.8084068
X-RAY DIFFRACTIONf_dihedral_angle_d13.491811
X-RAY DIFFRACTIONf_chiral_restr0.053477
X-RAY DIFFRACTIONf_plane_restr0.005540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.99880.2191410.20253132X-RAY DIFFRACTION100
1.9988-2.05280.2021440.17573131X-RAY DIFFRACTION100
2.0528-2.11320.20571280.16023133X-RAY DIFFRACTION100
2.1132-2.18140.17841420.15893142X-RAY DIFFRACTION100
2.1814-2.25940.18921610.15323143X-RAY DIFFRACTION100
2.2594-2.34990.17841230.16043111X-RAY DIFFRACTION100
2.3499-2.45680.19921310.15693174X-RAY DIFFRACTION100
2.4568-2.58630.20271440.16623154X-RAY DIFFRACTION100
2.5863-2.74830.19781460.17893139X-RAY DIFFRACTION100
2.7483-2.96050.22581480.18533187X-RAY DIFFRACTION100
2.9605-3.25830.17861500.17193174X-RAY DIFFRACTION100
3.2583-3.72960.16131410.14633187X-RAY DIFFRACTION100
3.7296-4.69790.13941390.12193220X-RAY DIFFRACTION100
4.6979-42.90910.16831620.16073340X-RAY DIFFRACTION100
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)
17.00680.6297-3.37941.9268-0.18823.52780.13650.2380.0934-0.0634-0.03320.1430.0026-0.2787-0.07650.22890.0722-0.04860.13630.00590.1618-37.5938-13.9187-37.9757
21.12830.6173-0.31481.4579-0.66792.45590.0812-0.0659-0.05530.1452-0.0564-0.09220.0506-0.011-0.02950.16920.0402-0.04990.1774-0.00320.1752-39.8884-23.7729-17.0389
30.9739-0.2729-0.26241.4995-0.01821.75110.01420.03510.0766-0.007-0.0385-0.1557-0.08930.03360.01570.20990.033-0.00920.20510.0140.2363-33.885-8.1211-30.8114
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 109 )
2X-RAY DIFFRACTION2chain 'A' and (resid 110 through 280 )
3X-RAY DIFFRACTION3chain 'A' and (resid 281 through 394 )

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