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- PDB-6led: Structure of D-carbamoylase mutant from Nitratireductor indicus -

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Basic information

Entry
Database: PDB / ID: 6led
TitleStructure of D-carbamoylase mutant from Nitratireductor indicus
ComponentsN-carbamoyl-D-amino-acid hydrolase
KeywordsHYDROLASE / carbamoylase / hydantoinse process / D-amino acid / BIOSYNTHETIC PROTEIN
Function / homology: / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase / hydrolase activity / N-carbamoyl-D-amino-acid hydrolase
Function and homology information
Biological speciesNitratireductor indicus C115 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 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)69,5918
Polymers69,2182
Non-polymers3726
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-17 kcal/mol
Surface area21500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.992, 93.992, 247.443
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: 34609.125 Da / Num. of mol.: 2 / Mutation: R211G
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.: 6 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.28 Å3/Da / Density % sol: 46.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 4000, Sodium Phosphate, sodium chloride

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Data collection

DiffractionMean temperature: 200 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Nov 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.37→50 Å / Num. obs: 27278 / % possible obs: 99.9 % / Redundancy: 20.8 % / Biso Wilson estimate: 28.62 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 37.17
Reflection shellResolution: 2.37→2.45 Å / Redundancy: 18.1 % / Rmerge(I) obs: 0.626 / Num. unique obs: 2647 / % possible all: 99.6

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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: 2.37→50 Å / SU ML: 0.2359 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.1419
RfactorNum. reflection% reflection
Rfree0.2146 1340 4.91 %
Rwork0.1676 --
obs0.1699 27275 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 34.04 Å2
Refinement stepCycle: LAST / Resolution: 2.37→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4809 0 24 297 5130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00195016
X-RAY DIFFRACTIONf_angle_d0.50966781
X-RAY DIFFRACTIONf_chiral_restr0.0454721
X-RAY DIFFRACTIONf_plane_restr0.0037895
X-RAY DIFFRACTIONf_dihedral_angle_d22.7171878
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.450.25441360.19552505X-RAY DIFFRACTION99.59
2.45-2.550.23551290.18512537X-RAY DIFFRACTION99.96
2.55-2.670.25521450.19012512X-RAY DIFFRACTION100
2.67-2.810.2751140.1882572X-RAY DIFFRACTION100
2.81-2.980.23841330.17972540X-RAY DIFFRACTION100
2.98-3.210.23781360.17792570X-RAY DIFFRACTION100
3.21-3.530.22461190.16592603X-RAY DIFFRACTION99.96
3.53-4.050.16651400.14482601X-RAY DIFFRACTION100
4.05-5.090.18061560.13582644X-RAY DIFFRACTION100
5.1-40.830.22141320.18482851X-RAY DIFFRACTION99.7
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)
12.086418833181.054410639651.632896888754.06564065768-0.3332765728571.660826889650.0413895054456-0.499682436380.1608486483230.2467838086140.037999443863-0.156156349379-0.008774153319040.368588095417-0.002853668175620.194664404990.0577469135634-0.04557699439770.1920145528680.003036437647690.1315414622626.617706340120.0872546533-1.2090219676
22.45455618934-0.232730643485-0.3629882577722.48944548752-0.5675626751372.98888695669-0.0201937062701-0.0524161045394-0.288937589420.04576769587030.139538861504-0.3506187032210.1817340577630.357136934255-0.1411703031030.1700592826640.0402044311047-0.03713847242090.21491969219-0.05490843298250.29175247907431.701324191112.5688365308-5.14226903424
33.58967922237-0.311338646743-2.186799245082.00911121910.5942498818277.418088690510.06736828590590.40762363617-0.580165677695-0.004221163142710.297337510483-0.09235478242510.9111859156530.243035443368-0.1517652257170.2729035651940.0528290322665-0.08019072065640.238199837471-0.06951828878250.33454930127324.31729408155.91424537951-10.2745006851
41.446388584920.04647915330830.09758822337182.322118092010.3188614996611.029616781450.01439506658650.185961412492-0.0770449890554-0.1008980376880.0591977274733-0.06483357041060.01503622692850.0285456399435-0.05859448522730.1460777431910.0107518154948-0.002552806339470.163765812987-0.01547980614150.1512434227718.524030196120.5078700424-11.8477802254
57.118923705171.279801494180.3888519832574.37064292076-0.2721780642215.489815078650.214002140789-1.444852266970.2254394665680.526405197436-0.0006102835689170.6249420345420.1213529905-0.698116997121-0.2289526256030.3547791259160.03900043724180.08235957267970.303982235132-0.05364612900540.2441157343618.8325252661623.87993666894.7314019143
62.83404582583-1.1404805219-4.473247621115.90873915413-1.038689213238.858068647570.0366775213373-0.495810185762-0.2899411739680.2181160672310.4423370702710.8283074057380.01852864959730.360237606753-0.4034874106830.23839194475-0.02178703718090.007061372626870.4142147850060.005701279875050.509064139931-3.9306774162517.8847176668-16.7988015206
71.67513645003-0.168908864771-0.337667926182.23133291130.03078956182572.021259308110.1720071290130.1536659714910.118238758212-0.149746873982-0.04642336606790.421029216705-0.0950248739983-0.360522797247-0.0910062605180.1841369835280.09421222626120.005832391112570.3294084876490.04557571602080.262669906266-15.283338023943.0805808941-19.6352529241
82.67278434964-0.338116171217-0.5942608237662.15956843889-0.2182973894472.29087334260.1263433658570.281114592202-0.247059486176-0.0622859392187-0.1408388914370.3938066826490.0622361625886-0.405693474258-0.02687322841920.1604787221030.046943709573-0.02240074532420.292797277768-0.00523926497560.244842122356-12.611333357632.1232583579-19.9952836632
93.88109398284-1.74579323731-1.392116913452.365991968151.331436664611.030310546720.0817696107440.128770188950.05176464492960.125059341702-0.1446767551510.05254340264670.055792996499-0.2667244700240.03071406606110.1600458594520.03368408345220.01216236788210.1812282486740.03688781534980.174483667204-1.090530419437.8994482648-12.6733172079
101.91474641303-1.875486713650.04215769435645.358345898770.01564057212350.7981528092990.2228126655420.312986036746-0.090130007362-0.199512248432-0.107778962105-0.2123621751920.09642786880430.0257240857496-0.129108768140.1532130175870.0138631974086-0.03950815248410.212400893115-0.01984041775440.2006982284915.7278148578328.7828865278-21.1696380767
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 87 )
3X-RAY DIFFRACTION3chain 'A' and (resid 88 through 114 )
4X-RAY DIFFRACTION4chain 'A' and (resid 115 through 266 )
5X-RAY DIFFRACTION5chain 'A' and (resid 267 through 284 )
6X-RAY DIFFRACTION6chain 'A' and (resid 285 through 307 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 74 )
8X-RAY DIFFRACTION8chain 'B' and (resid 75 through 208 )
9X-RAY DIFFRACTION9chain 'B' and (resid 209 through 251 )
10X-RAY DIFFRACTION10chain 'B' and (resid 252 through 307 )

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