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- PDB-1xrf: The Crystal Structure of a Novel, Latent Dihydroorotase from Aqui... -

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Basic information

Entry
Database: PDB / ID: 1xrf
TitleThe Crystal Structure of a Novel, Latent Dihydroorotase from Aquifex aeolicus at 1.7 A resolution
ComponentsDihydroorotase
KeywordsHYDROLASE / Dihydroorotase / Amidohydrolase / Metalloenzyme / Pyrimidine
Function / homology
Function and homology information


allantoinase activity / dihydroorotase / purine nucleobase catabolic process / dihydroorotase activity / 'de novo' UMP biosynthetic process / zinc ion binding / cytoplasm
Similarity search - Function
Dihydroorotase / Dihydroorotase signature 1. / Dihydroorotase signature 2. / 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 ...Dihydroorotase / Dihydroorotase signature 1. / Dihydroorotase signature 2. / 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 speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsMartin, P.D. / Purcarea, C. / Zhang, P. / Vaishnav, A. / Sadecki, S. / Guy-Evans, H.I. / Evans, D.R. / Edwards, B.F.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: The crystal structure of a novel, latent dihydroorotase from Aquifex aeolicus at 1.7A resolution
Authors: Martin, P.D. / Purcarea, C. / Zhang, P. / Vaishnav, A. / Sadecki, S. / Guy-Evans, H.I. / Evans, D.R. / Edwards, B.F.
History
DepositionOct 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydroorotase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0093
Polymers51,8481
Non-polymers1612
Water7,404411
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.579, 172.715, 59.336
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
11A-1760-

HOH

21A-1784-

HOH

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Components

#1: Protein Dihydroorotase / DHOase


Mass: 51847.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: pyrC / Production host: Escherichia coli (E. coli) / References: UniProt: O66990, dihydroorotase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.53 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: ethanol, peg 400, acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.9587, 0.9806, 0.9808
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 12, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95871
20.98061
30.98081
ReflectionResolution: 1.65→18.5 Å / Num. all: 56259 / Num. obs: 47187 / % possible obs: 83.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.09
Reflection shellResolution: 1.65→1.693 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 5599 / Rsym value: 0.879 / % possible all: 80

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: MAD / Resolution: 1.65→18.5 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.158 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.096 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21259 2527 5.1 %RANDOM
Rwork0.17705 ---
all0.17881 56259 --
obs0.17881 47187 87.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.845 Å2
Baniso -1Baniso -2Baniso -3
1--1.51 Å20 Å20 Å2
2---0.99 Å20 Å2
3---2.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.098 Å0.096 Å
Luzzati sigma a-0.069 Å
Refinement stepCycle: LAST / Resolution: 1.65→18.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2803 0 6 411 3220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222853
X-RAY DIFFRACTIONr_bond_other_d0.0020.022700
X-RAY DIFFRACTIONr_angle_refined_deg1.8581.9783854
X-RAY DIFFRACTIONr_angle_other_deg0.91536322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.045359
X-RAY DIFFRACTIONr_chiral_restr0.120.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023073
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02500
X-RAY DIFFRACTIONr_nbd_refined0.2180.2605
X-RAY DIFFRACTIONr_nbd_other0.2480.23252
X-RAY DIFFRACTIONr_nbtor_other0.0890.21774
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2440.2244
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2850.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3090.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4460.210
X-RAY DIFFRACTIONr_mcbond_it1.4021.51798
X-RAY DIFFRACTIONr_mcangle_it2.55622922
X-RAY DIFFRACTIONr_scbond_it3.92731055
X-RAY DIFFRACTIONr_scangle_it6.764.5932
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.473 134
Rwork0.432 2549
Refinement TLS params.Method: refined / Origin x: 20.083 Å / Origin y: 26.921 Å / Origin z: 25.966 Å
111213212223313233
T0.1369 Å2-0.0051 Å2-0.0091 Å2-0.123 Å20.017 Å2--0.0029 Å2
L0.5227 °2-0.1436 °20.1667 °2-0.3612 °2-0.0164 °2--0.22 °2
S0.0067 Å °-0.0429 Å °-0.0345 Å °-0.0002 Å °-0.0174 Å °-0.0252 Å °0.0395 Å °-0.0164 Å °0.0106 Å °

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