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- PDB-4pxe: The crystal structure of AtUAH in complex with glyoxylate -

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Basic information

Entry
Database: PDB / ID: 4pxe
TitleThe crystal structure of AtUAH in complex with glyoxylate
ComponentsUreidoglycolate hydrolase
KeywordsHYDROLASE / Amidase / Hydantoinase / Carbarmoylase
Function / homology
Function and homology information


ureidoglycolate amidohydrolase / ureide catabolic process / ureidoglycolate hydrolase activity / allantoin catabolic process / purine nucleobase catabolic process / plastid / manganese ion binding / endoplasmic reticulum
Similarity search - Function
Amidase, carbamoylase-type / Alpha-Beta Plaits - #360 / Bacterial exopeptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLYOXYLIC ACID / : / Ureidoglycolate hydrolase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.449 Å
AuthorsShin, I. / Rhee, S.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Structural insights into the substrate specificity of (s)-ureidoglycolate amidohydrolase and its comparison with allantoate amidohydrolase.
Authors: Shin, I. / Han, K. / Rhee, S.
History
DepositionMar 23, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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: Ureidoglycolate hydrolase
B: Ureidoglycolate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0258
Polymers92,6582
Non-polymers3686
Water23,3651297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-50 kcal/mol
Surface area30380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.983, 89.758, 163.932
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ureidoglycolate hydrolase / / AtUAH / Allantoate amidohydrolase 2 / AtAHH2 / Ureidoglycolate amidohydrolase


Mass: 46328.801 Da / Num. of mol.: 2 / Fragment: UNP residues 50-476
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: UAH, AAH2, At5g43600, K9D7.10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VXY9, EC: 3.5.3.19
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-GLV / GLYOXYLIC ACID / GLYOXALATE / GLYOXYLATE / Glyoxylic acid


Mass: 74.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H2O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1297 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.73 % / Mosaicity: 0.249 ° / Mosaicity esd: 0.002 °

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-1A11.1
SYNCHROTRONPhoton Factory AR-NW12A20.97923, 0.97940, 0.96417
Detector
TypeIDDetectorDate
DECTRIS PILATUS 2M-F1PIXELOct 27, 2012
ADSC QUANTUM 2102CCDMar 7, 2012
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.979231
30.97941
40.964171
ReflectionResolution: 1.449→50 Å / Num. obs: 182920 / % possible obs: 100 % / Redundancy: 8.7 % / Biso Wilson estimate: 16.17 Å2 / Rmerge(I) obs: 0.114 / Χ2: 0.939 / Net I/σ(I): 5.2
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.449-1.58.70.868180970.552100
1.5-1.568.80.67181410.583100
1.56-1.638.30.465181440.617100
1.63-1.7290.354181370.645100
1.72-1.838.70.261181630.735100
1.83-1.978.70.19181910.934100
1.97-2.178.90.148182751.144100
2.17-2.488.60.125183591.27100
2.48-3.128.60.101184451.397100
3.12-508.90.077189681.46799.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MAD / Resolution: 1.449→46.675 Å / SU ML: 0.3 / σ(F): 1.35 / Phase error: 15.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1759 2000 1.09 %
Rwork0.1615 --
obs0.1616 182800 99.84 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.442 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso max: 88.72 Å2 / Biso mean: 20.7487 Å2 / Biso min: 7.83 Å2
Baniso -1Baniso -2Baniso -3
1-2.528 Å20 Å2-0 Å2
2--1.1383 Å2-0 Å2
3----3.6663 Å2
Refinement stepCycle: LAST / Resolution: 1.449→46.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6404 0 14 1297 7715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066548
X-RAY DIFFRACTIONf_angle_d1.138860
X-RAY DIFFRACTIONf_chiral_restr0.0721028
X-RAY DIFFRACTIONf_plane_restr0.0061150
X-RAY DIFFRACTIONf_dihedral_angle_d11.7442456
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4493-1.48560.28381390.2679125601269998
1.4856-1.52580.24181420.23021281012952100
1.5258-1.57070.22151410.2021279912940100
1.5707-1.62140.18561420.17851283912981100
1.6214-1.67930.18041420.16591281712959100
1.6793-1.74660.18351430.15941286713010100
1.7466-1.8260.18761410.15611283912980100
1.826-1.92230.16541430.14961287413017100
1.9223-2.04280.17571430.15161289813041100
2.0428-2.20050.17131420.15021294413086100
2.2005-2.42190.15821440.15391296213106100
2.4219-2.77230.1871440.1581301313157100
2.7723-3.49270.18411450.16011308913234100
3.4927-46.6990.15321490.15611348913638100
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)
10.37830.02640.04570.5004-0.01460.2550.01650.03750.0016-0.08610.00620.1040.0924-0.04610.00040.1552-0.0198-0.01390.12170.00380.1375-2.888672.440390.2088
20.4527-0.34270.0660.3073-0.16750.66110.01990.0045-0.2124-0.08350.00720.03530.3735-0.12060.02620.3018-0.0611-0.00230.12770.00480.1924-2.620756.049896.9256
30.04670.0324-0.07830.1005-0.17250.6099-0.0221-0.017-0.0266-0.0351-0.0529-0.03630.09620.0938-0.00040.13060.02390.02960.13560.02190.142212.333964.1706118.4609
4-0.01570.0920.0929-0.00760.10180.1498-0.0220.0278-0.0141-0.07990.0223-0.00750.151-0.00920.00120.19610.0510.0560.13710.02150.157814.209663.192898.8254
50.10050.0938-0.08930.2057-0.24730.2178-0.003-0.02140.0045-0.0408-0.020.00470.05130.0221-00.15030.00640.0180.11540.00620.124511.515574.762995.873
60.17950.04150.01070.115-0.06880.0517-0.08460.00360.0426-0.04760.1627-0.02960.05120.179300.1747-0.00290.01660.1451-0.00110.12998.756577.784181.9692
70.35670.1009-0.25640.4406-0.03060.26830.0105-0.08760.00640.0644-0.0292-0.06050.00630.0711-0.00110.0953-0.0004-0.00680.14630.01260.1233-24.36263.174146.345
80.6266-0.2527-0.20580.393-0.15280.45090.0465-0.07790.19430.09840.0036-0.0893-0.15850.0720.01540.1434-0.03380.00850.1173-0.02940.1561-20.18479.675141.981
90.1619-0.0549-0.25860.06740.1780.56960.02130.01780.00630.0199-0.03310.0239-0.0617-0.0633-00.11640.01140.00990.1233-0.00520.12345.92871.639135.2
100.09330.0822-0.03970.1492-0.1070.09070.05790.03790.046-0.0713-0.0187-0.0296-0.1498-0.0056-0.00020.10190.01020.00880.13080.00450.1122-5.70472.259151.178
110.30560.0384-0.02820.31520.12690.2213-0.01080.0065-0.00490.0152-0.01520.01750.0039-0.002400.09150.00310.01080.11090.0090.1153-13.0659.852153.887
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 54:192)A54 - 192
2X-RAY DIFFRACTION2chain 'A' and (resseq 193:255)A193 - 255
3X-RAY DIFFRACTION3chain 'A' and (resseq 256:378)A256 - 378
4X-RAY DIFFRACTION4chain 'A' and (resseq 379:410)A379 - 410
5X-RAY DIFFRACTION5chain 'A' and (resseq 411:455)A411 - 455
6X-RAY DIFFRACTION6chain 'A' and (resseq 456:476)A456 - 476
7X-RAY DIFFRACTION7chain 'B' and (resseq 54:192)B54 - 192
8X-RAY DIFFRACTION8chain 'B' and (resseq 193:255)B193 - 255
9X-RAY DIFFRACTION9chain 'B' and (resseq 256:378)B256 - 378
10X-RAY DIFFRACTION10chain 'B' and (resseq 379:410)B379 - 410
11X-RAY DIFFRACTION11chain 'B' and (resseq 411:476)B411 - 476

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