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- PDB-3hm7: Crystal structure of allantoinase from Bacillus halodurans C-125 -

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Basic information

Entry
Database: PDB / ID: 3hm7
TitleCrystal structure of allantoinase from Bacillus halodurans C-125
ComponentsAllantoinase
KeywordsHYDROLASE / ALLANTOINASE / METALLO-DEPENDENT HYDROLASE / PROTEIN STRUCTURE INITIATIVE / PSI-2 / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / STRUCTURAL GENOMICS / DNA-BINDING / Metal-binding / Purine metabolism / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


allantoinase / allantoinase activity / allantoin catabolic process / cobalt ion binding / purine nucleobase metabolic process / zinc ion binding
Similarity search - Function
Allantoinase / Dihydroorotase, conserved site / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll ...Allantoinase / Dihydroorotase, conserved site / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsPatskovsky, Y. / Romero, R. / Rutter, M. / Miller, S. / Wasserman, S.R. / Sauder, J.M. / Raushel, F.M. / Burley, S.K. / Almo, S.C. / New York Structural GenomiX Research Consortium (NYSGXRC) / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of Allantoinase from Bacillus Halodurans
Authors: Patskovsky, Y. / Romero, R. / Rutter, M. / Miller, S. / Raushel, F.M. / Wasserman, S.R. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionMay 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Allantoinase
B: Allantoinase
C: Allantoinase
D: Allantoinase
E: Allantoinase
F: Allantoinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,30312
Polymers298,9116
Non-polymers3926
Water6,684371
1
A: Allantoinase
B: Allantoinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,7684
Polymers99,6372
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-85 kcal/mol
Surface area30830 Å2
MethodPISA
2
C: Allantoinase
hetero molecules

D: Allantoinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,7684
Polymers99,6372
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+4/31
Buried area2020 Å2
ΔGint-86 kcal/mol
Surface area30580 Å2
MethodPISA
3
E: Allantoinase
F: Allantoinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,7684
Polymers99,6372
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-84 kcal/mol
Surface area30430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.658, 157.658, 418.026
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31E
41F
51C
61D
DetailsAUTHOR STATES THAT THE ASSEMBLY IS LIKELY A TETRAMER. THE ASU CONTAINS 1 FULL TETRAMER - MONOMERS A,B,E,F AND ANOTHER HALF (MONOMERS C AND D). THE REASON - AT LEAST TWO SIMILAR ENZYMES HAVE SIMILAR ASSEMBLIES DESPITE DIFFERENT CRYSTAL PACKING. IT WAS NOT EXPERIMENTALLY VERIFIED, HOWEVER.

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Components

#1: Protein
Allantoinase / / Allantoin-utilizing enzyme


Mass: 49818.484 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Gene: allB, pucH, BH2309 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KAH8, allantoinase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 2.52 Å3/Da / Density % sol: 51.22 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100MM HEPES PH 7.5, 36% PEG 400, 300MM MAGNESIUM CHLORIDE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 4, 2008
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 94850 / % possible obs: 99.9 % / Observed criterion σ(I): -0.5 / Redundancy: 12.3 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 4
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.5 / % possible all: 100

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Processing

Software
NameVersionClassification
SHELXDphasing
RESOLVEmodel building
REFMAC5.3.0034refinement
HKL-2000data reduction
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.933 / SU B: 26.152 / SU ML: 0.268 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.015 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2673 2847 3 %RANDOM
Rwork0.23969 ---
obs0.24054 91704 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.874 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20.75 Å20 Å2
2--1.5 Å20 Å2
3----2.25 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20369 0 6 371 20746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02220995
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.95928467
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35152652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.40123.96942
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.845153625
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.91615134
X-RAY DIFFRACTIONr_chiral_restr0.0830.23184
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215898
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1430.310272
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.514072
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.51405
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1130.379
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.520
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.4642.513432
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.752421142
X-RAY DIFFRACTIONr_scbond_it9.16848453
X-RAY DIFFRACTIONr_scangle_it10.5416.57313
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3335 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.410.5
medium positional0.350
medium positional0.360
medium positional0.370
medium positional0.50
medium positional0.410
medium thermal5.9510
medium thermal5.140
medium thermal4.740
medium thermal4.730
medium thermal7.450
medium thermal5.890
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 178 -
Rwork0.27 6574 -
obs--99.93 %
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)
11.43490.03570.40371.65690.60484.63860.244-0.165-0.32660.17080.1934-0.30330.99160.5933-0.4374-0.02330.0813-0.173-0.012-0.0031-0.094810.986327.6034232.1881
21.27220.29050.14062.4271-0.26783.41210.07710.009-0.1599-0.3670.07160.26170.7392-0.2827-0.1487-0.0444-0.0429-0.1158-0.2476-0.0186-0.1347-8.409326.2866184.7021
30.87430.07980.55931.6444-0.82571.77620.00250.0370.1998-0.1505-0.06560.1263-0.28450.00250.06310.29250.15370.11060.22460.08860.123529.758687.0207255.593
43.5704-0.8569-2.44981.78410.99794.1415-0.0914-0.0433-0.32-0.00840.0376-0.02740.2923-0.12850.0538-0.1511-0.0462-0.0151-0.1488-0.0604-0.122950.840450.5342254.9627
51.60810.0191-0.61681.4543-0.3812.48030.1443-0.22680.28190.21780.05130.1884-0.3994-0.0779-0.1955-0.230900.0907-0.2396-0.0704-0.1574-11.233563.3454232.0909
61.2902-0.0913-0.25562.09450.02952.14820.01940.05050.1657-0.26010.0426-0.2755-0.1740.1972-0.062-0.25590.00620.0865-0.30310.0416-0.13959.371564.4319185.0674
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 438
2X-RAY DIFFRACTION2B3 - 438
3X-RAY DIFFRACTION3C3 - 437
4X-RAY DIFFRACTION4D3 - 438
5X-RAY DIFFRACTION5E3 - 438
6X-RAY DIFFRACTION6F3 - 438

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