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- PDB-6c0d: Crystal structure of an Amidase (hydantoinase/carbamoylase family... -

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Basic information

Entry
Database: PDB / ID: 6c0d
TitleCrystal structure of an Amidase (hydantoinase/carbamoylase family) from Burkholderia phymatum
ComponentsAmidase, hydantoinase/carbamoylase family
KeywordsHYDROLASE / SSGCID / Structural genomics / Burkholderia phymatum / amidase / hydrantoinase family / carbamoylase family / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


N-carbamoyl-L-amino-acid hydrolase / N-carbamoyl-L-amino-acid hydrolase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines / metal ion binding
Similarity search - Function
Amidase, carbamoylase-type / Bacterial exopeptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Amidase, hydantoinase/carbamoylase family
Similarity search - Component
Biological speciesParaburkholderia phymatum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of an Amidase (hydantoinase/carbamoylase family) from Burkholderia phymatum
Authors: Abendroth, J. / Conrady, D.G. / Lorimer, D.D. / Edwards, T.E.
History
DepositionDec 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amidase, hydantoinase/carbamoylase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,29912
Polymers45,3681
Non-polymers93011
Water8,701483
1
A: Amidase, hydantoinase/carbamoylase family
hetero molecules

A: Amidase, hydantoinase/carbamoylase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,59724
Polymers90,7372
Non-polymers1,86122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_764-x+2,-x+y+1,-z-1/31
Buried area7950 Å2
ΔGint-97 kcal/mol
Surface area31010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.620, 136.620, 67.510
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-753-

HOH

21A-1083-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Amidase, hydantoinase/carbamoylase family


Mass: 45368.262 Da / Num. of mol.: 1 / Fragment: BuphA.12245.b.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paraburkholderia phymatum (strain DSM 17167 / CIP 108236 / LMG 21445 / STM815) (bacteria)
Strain: DSM 17167 / CIP 108236 / LMG 21445 / STM815 / Gene: Bphy_4610 / Plasmid: BuphA.12245.b.B1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B2JR29, N-carbamoyl-L-amino-acid hydrolase

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Non-polymers , 5 types, 494 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / 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: 4.01 Å3/Da / Density % sol: 69.38 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Microlytic MCSG-1 screen F11: 200mM Ammonium sulfate, 25% PEG 3350, 100mM HEPES free acid / NaOH pH 7.5: BuphA.12245.b.B1.PW38373 at 22.42mg/ml: cryo: 15% EG in 2 steps: tray 296390 f11: puck jzk7-6.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→44.719 Å / Num. obs: 67274 / % possible obs: 100 % / Redundancy: 7.405 % / Biso Wilson estimate: 23.27 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.067 / Χ2: 1.066 / Net I/σ(I): 17.25
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.854.4320.5452.0849470.8280.62100
1.85-1.94.5970.4572.5747940.8910.518100
1.9-1.954.7660.3623.3347140.9290.407100
1.95-2.014.9390.2854.5145200.950.319100
2.01-2.085.1070.235.8443940.9660.25699.9
2.08-2.155.7070.1828.1442770.9820.201100
2.15-2.236.7260.16310.4141300.9880.177100
2.23-2.327.0860.14212.1539760.9910.154100
2.32-2.437.4890.12514.2138150.9940.13599.9
2.43-2.557.9650.10816.8736280.9950.11699.9
2.55-2.688.6450.09420.1234750.9970.199.9
2.68-2.8510.0760.08125.3332860.9980.085100
2.85-3.0410.8710.07229.0431110.9980.075100
3.04-3.2910.8550.06133.5628750.9990.065100
3.29-3.610.7670.05138.9326760.9990.054100
3.6-4.0210.660.04743.3124240.9990.049100
4.02-4.6510.6250.04345.6221440.9990.045100
4.65-5.6910.7720.03945.8218310.9990.041100
5.69-8.0510.80.03744.3114330.9990.039100
8.05-44.71910.1410.03148.518240.9990.03299

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MoRDaphasing
PHASERphasing
PARROTphasing
ARP/wARPmodel building
Cootmodel building
PHENIX1.13rc1_2961refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5j4mA as per MorDa

Resolution: 1.8→44.719 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.56
RfactorNum. reflection% reflectionSelection details
Rfree0.1775 1991 2.96 %0
Rwork0.1574 ---
obs0.158 67230 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.81 Å2 / Biso mean: 32.1336 Å2 / Biso min: 10.68 Å2
Refinement stepCycle: final / Resolution: 1.8→44.719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3013 0 58 500 3571
Biso mean--56.88 43.46 -
Num. residues----404
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8001-1.84510.26461340.226546404774
1.8451-1.8950.19911440.209946244768
1.895-1.95080.22271450.196946254770
1.9508-2.01370.22391690.177345644733
2.0137-2.08570.19891680.163946394807
2.0857-2.16920.17391620.158246024764
2.1692-2.26790.19771460.165346144760
2.2679-2.38750.19951290.163446474776
2.3875-2.5370.20451090.16746964805
2.537-2.73290.17041600.159246284788
2.7329-3.00790.18181450.16246624807
3.0079-3.4430.19441000.151347234823
3.443-4.33720.13141190.13347394858
4.3372-44.73320.16091610.147848364997
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)
11.8647-0.2235-0.03841.89330.0313.144-0.0003-0.00270.4069-0.1915-0.0201-0.1018-0.76070.0763-0.00130.3077-0.00690.00160.1406-0.00480.251463.085364.13939.3074
22.40491.2036-1.0650.6264-0.50950.46240.1222-0.22490.08140.0681-0.08070.0001-0.09350.1806-0.04360.1487-0.04980.00920.2164-0.00290.167995.875360.37660.3062
32.50930.18660.24941.52391.07012.1382-0.03430.07490.1515-0.23680.0009-0.0132-0.30550.21760.03150.1427-0.01160.00120.12570.02430.14367.399450.24176.6279
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 198 )A3 - 198
2X-RAY DIFFRACTION2chain 'A' and (resid 199 through 345 )A199 - 345
3X-RAY DIFFRACTION3chain 'A' and (resid 346 through 413 )A346 - 413

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