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

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Basic information

Entry
Database: PDB / ID: 6lcg
TitleStructure of D-carbamoylase mutant 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 / DI(HYDROXYETHYL)ETHER / N-carbamoyl-D-amino-acid hydrolase
Function and homology information
Biological speciesNitratireductor indicus C115 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLiu, Y.F. / Ni, Y. / Xu, G.C. / Dai, W.
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 18, 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

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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)69,5154
Polymers69,3022
Non-polymers2122
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-29 kcal/mol
Surface area22810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.650, 95.650, 261.621
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: 34651.160 Da / Num. of mol.: 2 / Mutation: D187N, A200N, 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.49 Å3/Da / Density % sol: 50.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 4000, Sodium Chlorium, Tris-HCl

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 18-ID / Wavelength: 0.987 Å
DetectorType: Bruker AXIOM 200 / 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: 2.7→47.82 Å / Num. obs: 20291 / % possible obs: 99.7 % / Redundancy: 21 % / Rmerge(I) obs: 0.229 / Net I/σ(I): 1.51
Reflection shellResolution: 2.7→2.83 Å / Rmerge(I) obs: 2.257 / Num. unique obs: 2616 / % possible all: 99.7

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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: 2.7→47.82 Å / SU ML: 0.4972 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.0727
RfactorNum. reflection% reflection
Rfree0.2655 1003 4.95 %
Rwork0.216 --
obs0.2184 20275 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→47.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4800 0 14 35 4849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00174920
X-RAY DIFFRACTIONf_angle_d0.42626634
X-RAY DIFFRACTIONf_chiral_restr0.0428698
X-RAY DIFFRACTIONf_plane_restr0.0038876
X-RAY DIFFRACTIONf_dihedral_angle_d21.09981824
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.840.40631590.34632647X-RAY DIFFRACTION99.12
2.84-3.020.35911260.29882684X-RAY DIFFRACTION99.5
3.02-3.250.3331540.28622684X-RAY DIFFRACTION99.75
3.25-3.580.32281440.25812708X-RAY DIFFRACTION99.79
3.58-4.10.27961280.20912761X-RAY DIFFRACTION99.86
4.1-5.160.2311360.17292798X-RAY DIFFRACTION99.86
5.16-47.820.21231560.19112990X-RAY DIFFRACTION99.81
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)
16.31078410262-5.298392356054.194093602764.88851165665-4.926304884798.09452870913-0.5519417789840.355007150288-0.6453085812390.6228927192680.4256009995050.534744052096-0.831867749719-0.187586690404-0.4902222819190.569370616787-0.189545709124-0.05780879235330.663061605948-0.01077006820620.693288947775-31.0254708469-19.606527896-3.46280970729
23.17825295992-0.70172062432-0.3421164051092.748058709921.119456978224.017026209130.0428755406180.400555631612-0.0102880638124-0.38021756547-0.1367439864770.260606609409-0.093645390522-0.5722577369580.123746483030.552885558817-0.0161587440528-0.05009396295520.480239895277-0.0001814243945810.535797038126-26.5719343549-11.7019784677-10.9630981954
36.91516484831-2.53500736249-0.2620717092194.0996122531-0.492126853183.26647687274-0.1871907263280.247396875835-0.666032619844-0.2513424099560.05079514597160.4178627677610.872091552412-0.4169065316450.09352083662990.640469610893-0.1094230784210.01126627975210.3327852893640.02604304482470.579597850919-22.9371184491-27.4172192012-10.1415527608
44.077532736113.72235478622-1.891352546386.33245267990.7205070885727.55832732760.0305486419346-1.19354180598-0.3463925816781.152691201470.164399602646-0.2497068768350.4008197238180.470501144273-0.2370244048350.948304694090.0916410168730.02967901257790.6202271351860.07826004716710.595553143372-15.6757310133-25.12626145363.95118965015
56.200147373890.0781881983785-0.9180252566164.684766570423.853705568583.37763201773-0.1136924093310.05216537870790.233682884515-0.0315722590980.588520547422-1.16324443410.1316897755211.0987698901-0.3722702151290.586968758651-0.100763074722-0.06754793450270.544273521157-0.110742897961.060893234641.98949388355-18.2428168556-12.9740646755
64.445403873561.34117136765-3.019456512686.539939717410.2327891483822.30164025628-0.8792609108590.0297531299995-0.470278947951-0.1716496694630.748448805233-0.7102961256991.220441766440.308975058851-0.04024194639890.9339702414390.2338210551080.1250879964550.60779779564-0.127952757340.5521435668596.17907434335-45.2433316668-19.6629458812
76.27646811066-1.466195349582.460836776475.079816566510.9786745444786.172926183490.332252703223-0.111490489824-0.842617729491-1.03989113683-0.0743840880235-0.2895417566091.525725266130.2871274192-0.3186665347861.146491461960.1431264019690.2137416448420.5144508059810.0904957096350.87999296307710.1613335122-47.299161847-21.3086610667
83.489943796950.368479963195-0.2591374581.74621074801-0.4438719714694.922096602780.06505105181220.0150578730431-0.0571188407212-0.28268778953-0.0446466965516-0.9074579707940.2997264622560.817077986306-0.00828975112690.702471809320.1309620690880.1961154469110.6271625688640.0622510686691.0245250576317.3037050617-35.2757524125-17.6417470686
94.24037975381-0.8215409597233.082000979166.1028130164-3.009199733443.97159439095-0.24066191921-0.4186426074270.5516963442570.452948402891-0.0938523563447-0.874076710368-0.239751053372-0.0004536312581630.3234902593650.645106208190.1221904899420.1013623869380.596615635531-0.1370481837220.87148937134111.159407524-30.2319426285-10.3014915908
103.0800235315-2.27730522337-1.641382518814.642345594863.217968063983.009144168710.03584280878740.01746734223290.086745885102-0.1832566986840.0926265422736-0.9210983285760.527354803857-0.539554413684-0.1294878039780.6958343826670.07554146163640.04676694285860.4746209405930.08593066746290.776896690220.916989625125-26.6746927528-18.2874626954
116.53633003938-1.39428560247-0.4181199866133.726000982382.088298962215.084489873090.285258553887-0.277829889489-0.03718576186750.02263352563490.1428827304690.3401451576250.6718979650810.041051225931-0.4829876424960.691017304374-0.071435068009-0.02235708266820.410460148951-0.01476265250010.59612851967-3.9901628501-34.9405772411-12.5523215313
127.80459307411-1.805967935131.712489731795.04807918218-0.8642866901325.52406449489-0.0629052412695-0.0613757348607-0.5711374816120.4126509328890.0733685878541-0.3646716784531.30693461780.102286576331-0.03661417177240.9102180967160.08383606210810.04011821398590.410208046797-0.008687355982210.49193651812-1.43478947035-42.4104651335-14.4525832672
136.38923157347-3.827662062833.735552747942.09493171456-6.355941023774.41321718082-0.1263236027010.250661049537-0.614356984983-0.2770508907680.64218299410.4341253641740.648265330685-0.822448175014-0.3885133613561.01940103005-0.009576985421830.04538686288220.677987080060.01607332637840.638531340928-8.00312157004-36.4842897278-28.8056922961
147.38985661183-5.135851745611.226332150158.2093632461-0.5505254973832.084643294690.6444399185170.325581594645-0.395799523695-0.5059879150420.3164693550820.0869481533699-0.170657939181-0.332958596084-0.9166011548630.666551624172-0.0585445326671-0.0149675084210.5532638147280.1291503949440.814252901358-7.74987247869-13.5008789451-17.8952164569
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 207 )
3X-RAY DIFFRACTION3chain 'A' and (resid 208 through 266 )
4X-RAY DIFFRACTION4chain 'A' and (resid 267 through 282 )
5X-RAY DIFFRACTION5chain 'A' and (resid 283 through 307 )
6X-RAY DIFFRACTION6chain 'B' and (resid 3 through 20 )
7X-RAY DIFFRACTION7chain 'B' and (resid 21 through 53 )
8X-RAY DIFFRACTION8chain 'B' and (resid 54 through 135 )
9X-RAY DIFFRACTION9chain 'B' and (resid 136 through 163 )
10X-RAY DIFFRACTION10chain 'B' and (resid 164 through 186 )
11X-RAY DIFFRACTION11chain 'B' and (resid 187 through 226 )
12X-RAY DIFFRACTION12chain 'B' and (resid 227 through 266 )
13X-RAY DIFFRACTION13chain 'B' and (resid 267 through 282 )
14X-RAY DIFFRACTION14chain 'B' and (resid 283 through 307 )

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