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- PDB-5i8i: Crystal Structure of the K. lactis Urea Amidolyase -

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Basic information

Entry
Database: PDB / ID: 5i8i
TitleCrystal Structure of the K. lactis Urea Amidolyase
ComponentsUrea Amidolyase
KeywordsHYDROLASE / hyrolase / biotin-dependent carboxylase
Function / homology
Function and homology information


urea carboxylase activity / methylcrotonoyl-CoA carboxylase activity / small molecule metabolic process / hydrolase activity / mitochondrion / ATP binding / metal ion binding
Similarity search - Function
Urea carboxylase / Allophanate hydrolase / : / Allophanate hydrolase C-terminal domain / 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 ...Urea carboxylase / Allophanate hydrolase / : / Allophanate hydrolase C-terminal domain / 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 / : / 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 / ATP-grasp fold / ATP-grasp fold profile. / Cyclophilin-like domain superfamily / Carbamoyl-phosphate synthase subdomain signature 2.
Similarity search - Domain/homology
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 6.5 Å
AuthorsZhao, J. / Xiang, S.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology of China2011CB910500 China
CitationJournal: Biosci. Rep. / Year: 2018
Title: Structure and function of urea amidolyase.
Authors: Zhao, J. / Zhu, L. / Fan, C. / Wu, Y. / Xiang, S.
History
DepositionFeb 19, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.title / _citation.year
Revision 1.3Nov 8, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Urea Amidolyase
B: Urea Amidolyase
C: Urea Amidolyase
D: Urea Amidolyase


Theoretical massNumber of molelcules
Total (without water)808,1064
Polymers808,1064
Non-polymers00
Water00
1
A: Urea Amidolyase
B: Urea Amidolyase


Theoretical massNumber of molelcules
Total (without water)404,0532
Polymers404,0532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint-29 kcal/mol
Surface area122820 Å2
MethodPISA
2
C: Urea Amidolyase
D: Urea Amidolyase


Theoretical massNumber of molelcules
Total (without water)404,0532
Polymers404,0532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-28 kcal/mol
Surface area122630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.740, 181.940, 549.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: VAL / End label comp-ID: VAL

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1METMETchain AAA1 - 17371 - 1737
2SERSERchain BBB3 - 17373 - 1737
3METMETchain CCC1 - 17371 - 1737
4SERSERchain DDD3 - 17373 - 1737

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Components

#1: Protein
Urea Amidolyase / KLLA0E08119p


Mass: 202026.484 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: KLLA0_E08119g / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) star / References: UniProt: Q6CP22

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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: 3.27 Å3/Da / Density % sol: 62.41 % / Mosaicity: 0.7 °
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5
Details: 0.1M Tris/HCl (pH 7.5), 0.2M ammonium sulfate, 12% PEG 8000, 2% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 6.5→274.91 Å / Num. all: 20690 / Num. obs: 20690 / % possible obs: 95.6 % / Redundancy: 3.9 % / Biso Wilson estimate: 219.55 Å2 / Rpim(I) all: 0.066 / Rrim(I) all: 0.137 / Rsym value: 0.118 / Net I/av σ(I): 5.5 / Net I/σ(I): 8.3 / Num. measured all: 80051
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
6.5-6.8540.5811.31192029840.3240.6710.5812.297.1
6.85-7.273.90.4531.71115328800.2580.5260.4532.897.2
7.27-7.773.80.2812.61034526940.160.3260.2814.397.4
7.77-8.393.80.1993.8937924950.1150.2310.1995.896.9
8.39-9.193.70.1255.8832622790.0710.1450.1258.294.9
9.19-10.283.90.0857.5782220190.0460.0980.08511.892.8
10.28-11.8740.06410753618970.0350.0740.0641597.5
11.87-14.5340.069.4640516080.0330.0680.0616.597.1
14.53-20.5540.04911.9525113180.0280.0570.04917.998.5
20.55-29.983.70.0597.419145160.0370.070.05919.567.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata collection
SCALA3.3.22data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VA7, 4ISS

3va7

4iss


Resolution: 6.5→29.98 Å / SU ML: 0.99 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3022 1015 4.93 %Random
Rwork0.2776 19588 --
obs0.2789 20603 95.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 428.01 Å2 / Biso mean: 308.3873 Å2 / Biso min: 230.58 Å2
Refinement stepCycle: final / Resolution: 6.5→29.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms51722 0 0 0 51722
Num. residues----6636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00952890
X-RAY DIFFRACTIONf_angle_d1.63871812
X-RAY DIFFRACTIONf_chiral_restr0.0787988
X-RAY DIFFRACTIONf_plane_restr0.0089346
X-RAY DIFFRACTIONf_dihedral_angle_d17.88519624
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A31288X-RAY DIFFRACTION9.583TORSIONAL
12B31288X-RAY DIFFRACTION9.583TORSIONAL
13C31288X-RAY DIFFRACTION9.583TORSIONAL
14D31288X-RAY DIFFRACTION9.583TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
6.5001-6.8390.38091420.3442740288296
6.839-7.26180.36881370.32672801293897
7.2618-7.81330.36541270.30192789291697
7.8133-8.58280.30051540.28832771292596
8.5828-9.78670.30311590.25572661282092
9.7867-12.19070.25911400.23492855299596
12.1907-29.980.27931560.28062971312797
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)
1-0.4572-1.0645-1.08871.6905-2.91941.6247-0.63880.8788-0.3631-0.20760.9786-0.09170.73170.2711-02.88720.06530.04263.5943-0.19912.951810.4435-32.30390.4583
20.2706-0.35680.04770.42860.40660.8693-0.93580.43430.17640.60910.61571.7972-1.01470.950503.16550.2736-0.32893.62830.29493.4579-26.7936-6.40955.2179
31.63470.28291.51890.28990.66310.93721.0401-0.5508-0.8749-0.4875-0.24480.43650.9731-0.3265-03.4283-0.6793-0.20964.0336-0.03173.4256-38.728115.2789-33.6062
44.2568-2.26474.68442.4438-1.29492.84570.3947-0.2382-1.1932-0.44050.03940.28640.05970.151702.4964-0.36440.29232.97970.18823.301310.893929.5373-35.1699
51.74631.77960.59081.0772-1.78393.7876-0.3954-0.14710.09720.7760.1819-0.3283-0.79140.5412-02.4841-0.2354-0.12563.6094-0.03632.96825.141410.428116.1694
60.1713-0.44980.34330.55580.52641.17770.33912.191-2.0611.0708-0.8390.9241-0.7751-1.18203.35640.14710.12422.95320.08484.1587-20.039111.523916.2537
72.12441.09290.9088-1.08591.26481.42940.87870.12990.5423-0.074-0.20251.2621-1.2585-0.405703.94270.80420.16183.639-0.10313.8804-38.34871.80954.4392
82.2526-0.130.47081.51111.36574.2269-0.1191-0.4573-0.0680.27730.1515-0.4590.6677-0.27703.1055-0.04210.14812.86550.03543.2885-10.2193-41.484452.8404
91.7212-0.121.09040.59-0.82740.7030.03911.0297-0.0269-0.7676-0.2358-0.0271-1.21761.511604.2251-0.13790.4193.8358-0.23572.857111.798146.217-135.8449
100.62850.7299-0.08540.08890.85880.19931.8324-0.2763-0.29381.0607-1.0374-0.38440.422-0.560703.9295-0.0745-0.79962.88190.08623.4838-15.723810.0622-131.9628
11-0.69010.02440.39162.42321.75770.66910.1747-0.1975-0.83440.53690.14620.23791.49350.657404.27950.46310.30712.83530.34713.9402-30.67960.3714-172.7675
121.92220.95720.23772.21561.81413.8573-0.76780.12320.06280.03650.4039-0.4783-0.9874-0.5465-03.97160.3323-0.28623.09440.14063.3526-45.569849.7586-175.5233
131.9747-1.83540.29421.2538-0.53122.31090.41941.14260.1133-0.10650.02970.16160.9819-0.5383-03.6442-0.61940.05582.948-0.09393.6362-27.23182.7845-80.2693
140.9507-0.07630.13254.1074-1.2041.87730.060.29320.18850.3637-0.0996-0.03940.18410.576803.30890.0760.21343.3333-0.10062.923516.024830.9676-82.026
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resseq 1:481))A1 - 481
2X-RAY DIFFRACTION2chain 'A' and ((resseq 482:614))A482 - 614
3X-RAY DIFFRACTION3chain 'A' and ((resseq 621:1068))A621 - 1068
4X-RAY DIFFRACTION4chain 'A' and ((resseq 1069:1737))A1069 - 1737
5X-RAY DIFFRACTION5chain 'B' and ((resseq 3:481))B3 - 481
6X-RAY DIFFRACTION6chain 'B' and ((resseq 482:614))B482 - 614
7X-RAY DIFFRACTION7chain 'B' and ((resseq 621:1068))B621 - 1068
8X-RAY DIFFRACTION8chain 'B' and ((resseq 1069:1737))B1069 - 1737
9X-RAY DIFFRACTION9chain 'C' and ((resseq 1:481))C1 - 481
10X-RAY DIFFRACTION10chain 'C' and ((resseq 482:614))C482 - 614
11X-RAY DIFFRACTION11chain 'C' and ((resseq 621:1068))C621 - 1068
12X-RAY DIFFRACTION12chain 'C' and ((resseq 1069:1737))C1069 - 1737
13X-RAY DIFFRACTION13chain 'D' and ((resseq 621:1068))D621 - 1068
14X-RAY DIFFRACTION14chain 'D' and ((resseq 1069:1737))D1069 - 1737

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