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- PDB-6lei: Structure of D-carbamoylase from Nitratireductor indicus -

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Basic information

Entry
Database: PDB / ID: 6lei
TitleStructure of D-carbamoylase from Nitratireductor indicus
ComponentsN-carbamoyl-D-amino-acid hydrolase
KeywordsHYDROLASE / carbamoylase / hydantoinse process / D-amino acid / BIOSYNTHETIC PROTEIN
Function / homologybeta-alanine biosynthetic process via 3-ureidopropionate / beta-ureidopropionase activity / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase / N-carbamoyl-D-amino-acid hydrolase
Function and homology information
Biological speciesNitratireductor indicus C115 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNi, Y. / Liu, Y.F. / Xu, G.C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China China
CitationJournal: Acs Catalysis / Year: 2020
Title: Structure-Guided Engineering of D-Carbamoylase Reveals a Key Loop at Substrate Entrance Tunnel
Authors: Liu, Y. / Xu, G. / Zhou, J. / Ni, J. / Zhang, L. / Hou, X. / Yin, D. / Rao, Y. / Zhao, Y.L. / Ni, Y.
History
DepositionNov 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-carbamoyl-D-amino-acid hydrolase
B: N-carbamoyl-D-amino-acid hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7297
Polymers69,4192
Non-polymers3105
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-17 kcal/mol
Surface area21910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.617, 93.617, 246.321
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein N-carbamoyl-D-amino-acid hydrolase


Mass: 34709.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitratireductor indicus C115 (bacteria)
Gene: NA8A_19058 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: K2NMS4
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 4000, sodium chloride, Bis-Tris propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 18-ID / Wavelength: 0.987 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: May 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 16496 / % possible obs: 99.9 % / Redundancy: 42.1 % / Biso Wilson estimate: 35.82 Å2 / Rmerge(I) obs: 0.172 / Net I/σ(I): 41.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 43.6 % / Rmerge(I) obs: 0.679 / Mean I/σ(I) obs: 11.2 / Num. unique obs: 3316 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FO6

1fo6


Resolution: 2.8→42.1 Å / SU ML: 0.3241 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.3836
RfactorNum. reflection% reflection
Rfree0.2411 777 4.71 %
Rwork0.2019 --
obs0.2037 16495 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 38.83 Å2
Refinement stepCycle: LAST / Resolution: 2.8→42.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4858 0 20 183 5061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00164986
X-RAY DIFFRACTIONf_angle_d0.43686719
X-RAY DIFFRACTIONf_chiral_restr0.0427708
X-RAY DIFFRACTIONf_plane_restr0.0035887
X-RAY DIFFRACTIONf_dihedral_angle_d20.58911850
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.980.30841290.26192526X-RAY DIFFRACTION99.55
2.98-3.210.28731360.24272549X-RAY DIFFRACTION100
3.21-3.530.25651200.21562577X-RAY DIFFRACTION100
3.53-4.040.20891290.18342598X-RAY DIFFRACTION100
4.04-5.090.1741190.16022651X-RAY DIFFRACTION100
5.09-42.10.2661440.20972817X-RAY DIFFRACTION99.73
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)
12.718150464550.8260619087270.8628665548773.15945522175-0.2984088410612.55349198206-0.595067692988-0.5996316085080.1971087596840.3829497920080.5821382059110.01663708975490.515090962590.611046966887-0.0446273478950.2247105732930.06818811103670.04617773281730.207201634435-0.03722667066110.21622969375424.572602668319.8858378176-0.418510811217
26.65916885499-4.72655362899-7.405925835885.806594396436.227894301018.96631523258-0.385847862405-0.8545572883560.5294357614450.2052019653690.74543905393-0.498660774857-0.06071903192941.70305047656-0.0565103074050.326822452016-0.03817559819720.01799427854030.2562075840050.001358665780440.34775998205134.19848657416.93927051541.80741767452
32.626824625580.288872104015-0.4467861441132.6853042812-0.8192002992995.210423426310.1001580454980.1369890099010.00578334949063-0.2812237526940.156888898466-0.7323739110080.2386107285730.261504323259-0.2613738207160.2773901396567.17796364557E-50.07230344235990.225476673276-0.0847240811360.28337787098729.746164701912.7376438159-12.3487308881
42.39584069946-0.8402100460490.4793167166862.59957930021-0.928364296093.775291969690.01064261353110.138487994891-0.578754899243-0.1965495167330.245647742228-0.006815246268340.111255967038-0.029299549003-0.09181658218760.226268288064-0.05168520429550.05509402945840.169706467323-0.03575257219510.28307715671123.93199464967.63352231805-8.05606781758
53.60610828202-0.144578918202-1.206375287241.549908393690.6952978876053.492489756340.144292726820.1314129651970.132500719131-0.133548360173-0.1012973655880.108567007287-0.1419549744670.123252649735-0.03140859768320.2796902453940.00694699348323-0.04555435540960.1759210883580.003444411646820.16699786240316.558752554917.2551675594-14.2222585396
66.13858941566-3.15376934080.1218664567797.545320509990.724863343576.70270706598-0.210311158078-0.460921638830.0760545629065-0.5517677162870.0650396899637-0.5366126772380.1434605599520.8336088552630.1388489658330.2363928762140.02552850935520.002863590426190.164823309002-0.05373657940240.21473502107913.130254712430.137586784-11.6644564958
75.52613303973-1.30038680739-2.933038532033.161967202950.9199187637423.45833412549-0.07564831269580.169036564704-0.0439206320797-0.4152820553060.205134037597-0.0774277785773-0.3639466229490.153722007334-0.06114064980050.222839297352-0.0597730766523-0.02599221911260.196438024931-0.037527581920.15405791022323.501960909825.435274304-8.72428588916
84.87921630294-0.2846331635350.262221376472.86033606463-0.005539787390623.26701105976-0.181464204334-0.9649630667090.8721273912620.5323037364170.243015948010.442235370374-0.03588683526210.124338263024-0.1195295608620.3529533371480.01569749672650.08434908764250.25158511897-0.04647557619760.28199890825413.100770192626.45532437081.68826984269
93.36825425650.741108436341-2.563171066065.51149218454-2.846721030213.57599326931-0.0657628768048-0.358642694557-0.7005319518210.2052033245370.3948539839760.6407754938460.839635308110.205285309872-0.2949264623060.286831688377-0.0258178294298-0.02810392668470.3822420394740.01831232554970.563356537716-4.5720989235918.30126874-16.5845871344
101.712326560220.4437889718890.9866182972093.815678757620.2191944906571.49782378260.04545631452610.253532355260.181203779663-0.251608528089-0.1564962050310.277090976525-0.732875691353-0.326875606369-0.08492965736470.1508151645810.173789573848-0.01528447808960.3225502564750.1486216043570.279833263642-7.6026864556945.3743283707-22.0276126263
112.694702793690.0603545557693-0.969508471722.62824593728-1.035683706553.773231744140.1788397649860.1451946181320.348471259689-0.13507574435-0.05180186501460.588795186036-0.132203179608-0.609629240278-0.1371529029330.1738048904320.0686190557577-0.01464913420320.372830232979-0.01438759372530.318612554282-18.849010825743.1946788361-21.3946349575
123.81298538977-0.341735149895-1.801639726552.92351203612-0.3029277922865.411673844550.1896149298710.149832379196-0.4647554109760.0919544562099-0.3068993324890.450312466580.147710385001-0.466703354399-0.04102893155650.23507134054-0.0346837119744-0.09677238629470.339417526457-0.001964698360890.321835013106-16.923217592530.3701125943-19.4851850576
134.24327303807-1.56947837866-1.013147533124.726145801320.729373911194.061936015510.180656593133-0.246478466182-0.06831608178740.02828859406840.0121641254050.08368603788060.3057642515240.0193106042904-0.2175646225350.148701632357-0.02171396713540.02496391140050.1489260781330.01109562022220.220189034246-4.005610248131.3869267513-17.2140555929
147.63177621219-2.21071657678-0.2837296266343.717511473140.1207010183020.5082343901250.036801669792-0.3018219295710.04114325995590.340188885715-0.0394540246801-0.1693298057330.0697721541427-0.163608331847-0.03588817001880.207383464474-0.01847982962760.01474342637480.1706324410010.02726143979660.196375931277-1.3242419866138.1490229313-11.5112679025
152.36912549069-1.244193035330.6869662200245.62193084493-0.4297346313960.7147246504820.3516897365640.323352733038-0.129748863092-0.0932150760145-0.239750844829-0.02650435138460.1526771599130.0519730859607-0.0707168947870.247898921697-0.0376841021409-0.02310390479030.218983704331-0.04302370456110.1781024239775.261437394828.750403755-21.3384471056
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 37 )
3X-RAY DIFFRACTION3chain 'A' and (resid 38 through 74 )
4X-RAY DIFFRACTION4chain 'A' and (resid 75 through 135 )
5X-RAY DIFFRACTION5chain 'A' and (resid 136 through 207 )
6X-RAY DIFFRACTION6chain 'A' and (resid 208 through 226 )
7X-RAY DIFFRACTION7chain 'A' and (resid 227 through 251 )
8X-RAY DIFFRACTION8chain 'A' and (resid 252 through 283 )
9X-RAY DIFFRACTION9chain 'A' and (resid 284 through 307 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 20 )
11X-RAY DIFFRACTION11chain 'B' and (resid 21 through 87 )
12X-RAY DIFFRACTION12chain 'B' and (resid 88 through 163 )
13X-RAY DIFFRACTION13chain 'B' and (resid 164 through 205 )
14X-RAY DIFFRACTION14chain 'B' and (resid 206 through 251 )
15X-RAY DIFFRACTION15chain 'B' and (resid 252 through 307 )

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