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- PDB-4iss: SeMet-substituted Kluyveromyces lactis Allophanate Hydrolase -

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Basic information

Entry
Database: PDB / ID: 4iss
TitleSeMet-substituted Kluyveromyces lactis Allophanate Hydrolase
ComponentsAllophanate Hydrolase
KeywordsHYDROLASE / mixed alpha and beta structure / allophanate binding
Function / homology
Function and homology information


small molecule metabolic process / urea carboxylase activity / methylcrotonoyl-CoA carboxylase activity / propionyl-CoA carboxylase activity / hydrolase activity / mitochondrion / ATP binding / metal ion binding
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1700 / Urea carboxylase / Allophanate hydrolase / Carboxyltransferase domain, subdomain A and B / Carboxyltransferase domain, subdomain A and B / Allophanate hydrolase subunit 2 / Carboxyltransferase domain, subdomain C and D / Carboxyltransferase domain, subdomain C and D / Allophanate hydrolase subunit 1 / Gamma-glutamyl cyclotransferase-like ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1700 / Urea carboxylase / Allophanate hydrolase / Carboxyltransferase domain, subdomain A and B / Carboxyltransferase domain, subdomain A and B / Allophanate hydrolase subunit 2 / Carboxyltransferase domain, subdomain C and D / Carboxyltransferase domain, subdomain C and D / Allophanate hydrolase subunit 1 / Gamma-glutamyl cyclotransferase-like / Hypothetical upf0131 protein ytfp / Amidase signature (AS) enzymes / Amidase signature (AS) domain / Amidase signature domain / Amidase signature (AS) superfamily / Amidase / Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Carbamoyl-phosphate synthase subdomain signature 1. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Biotin-requiring enzyme / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Pre-ATP-grasp domain superfamily / Cyclophilin-like domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Carbamoyl-phosphate synthase subdomain signature 2. / Roll / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
D(-)-TARTARIC ACID / KLLA0E08119p
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsFan, C. / Xiang, S.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structure and function of allophanate hydrolase.
Authors: Fan, C. / Li, Z. / Yin, H. / Xiang, S.
History
DepositionJan 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Aug 7, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Allophanate Hydrolase
B: Allophanate Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,9224
Polymers141,6802
Non-polymers2422
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-29 kcal/mol
Surface area45380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.050, 107.720, 150.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 481
2114B1 - 481
1224A482 - 620
2224B482 - 620

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.405623, 0.544268, -0.734331), (0.533896, -0.511016, -0.67366), (-0.741906, -0.665309, -0.083303)173.6105, 4.53196, 143.41689

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Components

#1: Protein Allophanate Hydrolase / KLLA0E08119p


Mass: 70839.867 Da / Num. of mol.: 2 / Fragment: UNP residues 1-621
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast) / Gene: KLLA0E08119g, KLLA0_E08119g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CP22, allophanate hydrolase
#2: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.67 Å3/Da / Density % sol: 53.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 16% PEG8000, 20% glycerol, 0.04 M potassium phosphate monobasic, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 1, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 53115 / Num. obs: 53061 / % possible obs: 99.9 % / Redundancy: 6 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 6.1
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 6 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SnBphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→46.53 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.906 / SU B: 9.052 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.418 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24659 2715 5.1 %RANDOM
Rwork0.17623 ---
obs0.17978 50331 99.85 %-
all-50406 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.517 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2--0.11 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9479 0 16 273 9768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.029721
X-RAY DIFFRACTIONr_angle_refined_deg1.9771.98313231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.75951224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.34124.785395
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.213151600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0931540
X-RAY DIFFRACTIONr_chiral_restr0.1470.21497
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217332
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
13691MEDIUM POSITIONAL0.350.5
13691MEDIUM THERMAL4.812
21040MEDIUM POSITIONAL0.470.5
21040MEDIUM THERMAL8.82
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 196 -
Rwork0.262 3387 -
obs--99.97 %

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