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- PDB-1xrh: Crystal Structure of Ureidoglycolate Dehydrogenase from Escherich... -

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Basic information

Entry
Database: PDB / ID: 1xrh
TitleCrystal Structure of Ureidoglycolate Dehydrogenase from Escherichia Coli
ComponentsUreidoglycolate Dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / Protein Structure Initiative / NYSGXRC / T1456 / ALLD / GLXB8 / B0517 / Ureidoglycolate dehydrogenase / PSI / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


ureidoglycolate dehydrogenase (NAD+) / ureidoglycolate dehydrogenase activity / allantoin assimilation pathway / purine nucleobase metabolic process / cytoplasm
Similarity search - Function
Ureidoglycolate dehydrogenase / Malate/L-lactate dehydrogenase-like / Malate/L-sulfolactate/L-lactate dehydrogenase-like superfamily / Malate/L-sulfolactate/L-lactate dehydrogenase-like, NADPH binding domain / Malate/L-sulfolactate/L-lactate dehydrogenase-like, alpha-helical domain / Malate/L-lactate dehydrogenase / Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 / Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel / Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain / Ribosomal Protein S8; Chain: A, domain 1 ...Ureidoglycolate dehydrogenase / Malate/L-lactate dehydrogenase-like / Malate/L-sulfolactate/L-lactate dehydrogenase-like superfamily / Malate/L-sulfolactate/L-lactate dehydrogenase-like, NADPH binding domain / Malate/L-sulfolactate/L-lactate dehydrogenase-like, alpha-helical domain / Malate/L-lactate dehydrogenase / Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 / Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel / Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain / Ribosomal Protein S8; Chain: A, domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ureidoglycolate dehydrogenase (NAD(+))
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsRajashankar, K.R. / Kniewel, R. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of Ureidoglycolate Dehydrogenase from Escherichia Coli
Authors: Rajashankar, K.R. / Kniewel, R. / Lima, C.D.
History
DepositionOct 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 3, 2018Group: Data collection / Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Aug 23, 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
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ureidoglycolate Dehydrogenase
B: Ureidoglycolate Dehydrogenase
C: Ureidoglycolate Dehydrogenase
D: Ureidoglycolate Dehydrogenase
E: Ureidoglycolate Dehydrogenase
F: Ureidoglycolate Dehydrogenase
G: Ureidoglycolate Dehydrogenase
H: Ureidoglycolate Dehydrogenase


Theoretical massNumber of molelcules
Total (without water)309,5908
Polymers309,5908
Non-polymers00
Water11,602644
1
A: Ureidoglycolate Dehydrogenase
B: Ureidoglycolate Dehydrogenase


Theoretical massNumber of molelcules
Total (without water)77,3982
Polymers77,3982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-65 kcal/mol
Surface area25330 Å2
MethodPISA
2
C: Ureidoglycolate Dehydrogenase
D: Ureidoglycolate Dehydrogenase


Theoretical massNumber of molelcules
Total (without water)77,3982
Polymers77,3982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-67 kcal/mol
Surface area25830 Å2
MethodPISA
3
E: Ureidoglycolate Dehydrogenase
F: Ureidoglycolate Dehydrogenase


Theoretical massNumber of molelcules
Total (without water)77,3982
Polymers77,3982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-66 kcal/mol
Surface area25350 Å2
MethodPISA
4
G: Ureidoglycolate Dehydrogenase
H: Ureidoglycolate Dehydrogenase


Theoretical massNumber of molelcules
Total (without water)77,3982
Polymers77,3982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-64 kcal/mol
Surface area25190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.715, 129.916, 106.468
Angle α, β, γ (deg.)90.00, 95.77, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
DetailsThere are four biological units in the asymmetric unit. Polypeptide chains A and B together form a biological unit and so are CD, EF and GH.

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Components

#1: Protein
Ureidoglycolate Dehydrogenase / E.C.1.1.1.154


Mass: 38698.777 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ALLD / Plasmid: PET T7 / Production host: Escherichia coli (E. coli) / Strain (production host): B834, DE3 / References: UniProt: P77555, EC: 1.1.1.154
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 644 / 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: 2.38 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15% PEG 4000, 0.1M Sodium Citrate pH 5.6, 0.06M Amonium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 31, 2003 / Details: Diamond monochromator and downstream mirror
RadiationMonochromator: Flat Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.25→19.86 Å / Num. all: 213051 / Num. obs: 213051 / % possible obs: 80.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.2 % / Biso Wilson estimate: 25.6 Å2 / Rsym value: 0.078 / Net I/σ(I): 6.5
Reflection shellResolution: 2.25→2.33 Å / Num. unique all: 19123 / Rsym value: 0.284 / % possible all: 72

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
BEASTmodel building
SHARPphasing
RESOLVEmodel building
CNS1.1refinement
BEASTphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: Density modified experimental electron density map based on Se sites. Se sites were obtained from poor phases from a weak MR solution using a model derived from pdb entry 1RFM.

1rfm
PDB Unreleased entry


Resolution: 2.25→19.86 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 467989.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: See remarks 999 and 400
RfactorNum. reflection% reflectionSelection details
Rfree0.25 9082 4.5 %RANDOM
Rwork0.192 ---
obs0.1921 200433 75.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.6669 Å2 / ksol: 0.357724 e/Å3
Displacement parametersBiso mean: 38.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å21.74 Å2
2--3.28 Å20 Å2
3----2.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.25→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20836 0 0 644 21480
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d1.22
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.222
X-RAY DIFFRACTIONc_scbond_it3.092
X-RAY DIFFRACTIONc_scangle_it3.872.5
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.317 1141 4.3 %
Rwork0.282 25692 -
obs--60.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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