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- PDB-7k46: Crystal Structure of a putative aspartate carbamoyltransferase Le... -

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Basic information

Entry
Database: PDB / ID: 7k46
TitleCrystal Structure of a putative aspartate carbamoyltransferase Leishmania major Friedlin
ComponentsAspartate carbamoyltransferase
KeywordsTRANSFERASE / SSGCID / Aspartate carbamoyltransferase / Leishmania major / LMJF_16_0540 / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / glycosome / nuclear lumen / ciliary plasm / : / amino acid metabolic process / amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process ...aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / glycosome / nuclear lumen / ciliary plasm / : / amino acid metabolic process / amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / cytosol / cytoplasm
Similarity search - Function
Aspartate carbamoyltransferase / ACT domain profile. / ACT domain / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
Similarity search - Domain/homology
Aspartate carbamoyltransferase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of a putative aspartate carbamoyltransferase Leishmania major Friedlin
Authors: Abendroth, J.A. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionSep 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Aspartate carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3943
Polymers36,2701
Non-polymers1242
Water7,584421
1
A: Aspartate carbamoyltransferase
hetero molecules

A: Aspartate carbamoyltransferase
hetero molecules

A: Aspartate carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,1829
Polymers108,8103
Non-polymers3726
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation11_566y,-z+1,-x+11
Buried area6590 Å2
ΔGint3 kcal/mol
Surface area35020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.240, 136.240, 136.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-843-

HOH

21A-881-

HOH

31A-898-

HOH

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Components

#1: Protein Aspartate carbamoyltransferase / / LemaA.01332.a


Mass: 36269.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF_16_0540 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4QEW6, aspartate carbamoyltransferase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 421 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.91 Å3/Da / Density % sol: 57.7 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Microlytic MCSG1 screen, condition G7: 25% (w/V) PEG 3350, 100mM Tris base / HCl pH 8.5: LemaA.01332.a.AE1.PS38633 (originally labelled as MyavA.00358.f.AE1.PS38633) at 13.16mg/ml; tray ...Details: Microlytic MCSG1 screen, condition G7: 25% (w/V) PEG 3350, 100mM Tris base / HCl pH 8.5: LemaA.01332.a.AE1.PS38633 (originally labelled as MyavA.00358.f.AE1.PS38633) at 13.16mg/ml; tray 315258 G7; cryo: 20% EG in 2 steps; puck: ddy3-5. For phasing a crystal from the same tray, condition D4 (200mM sodium thiocyanate, 20% (w/V) PEG 3350) was soaked for 15 sec in a mix of 90% reservoir and 10% 2.5M NaI in EG, followed by a 15sec soak in a mix of 80% reservoir and 20% 2.5m NaI in EG: tray 315258 d4: puck ddy3-3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 33187 / % possible obs: 100 % / Redundancy: 15.975 % / Biso Wilson estimate: 30.123 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.061 / Χ2: 0.946 / Net I/σ(I): 32.55
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.959.6610.5634.2124360.9330.595100
1.95-29.9810.4385.4423630.9560.462100
2-2.0610.3470.3596.7823240.9710.378100
2.06-2.1210.9980.2679.422290.9840.28100
2.12-2.1913.10.20713.9721810.9920.215100
2.19-2.2714.1510.18116.820980.9950.18799.9
2.27-2.3614.6760.14920.2320450.9960.155100
2.36-2.4515.3120.12923.3219580.9980.13399.7
2.45-2.5616.0970.11426.2918610.9980.117100
2.56-2.6917.1690.09731.0718010.9990.1100
2.69-2.8318.9850.08236.8417220.9990.084100
2.83-322.0850.0745.2216060.9990.07299.9
3-3.2122.1860.05853.2815430.9990.06100
3.21-3.4722.130.04862.91142710.049100
3.47-3.821.9990.0474.93132410.041100
3.8-4.2521.8270.03683.37117910.037100
4.25-4.9121.7730.03387.5106810.034100
4.91-6.0121.9690.03577.3789710.036100
6.01-8.521.680.03478.4471510.035100
8.5-5019.6370.02493.441010.02599.3

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
PARROTphasing
ARP/wARPmodel building
CRANK2phasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.9→48.17 Å / SU ML: 0.1763 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.5641
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1758 1954 5.89 %0
Rwork0.1523 31224 --
obs0.1538 33178 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.42 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2314 0 8 421 2743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00622408
X-RAY DIFFRACTIONf_angle_d0.79423270
X-RAY DIFFRACTIONf_chiral_restr0.0529398
X-RAY DIFFRACTIONf_plane_restr0.0074418
X-RAY DIFFRACTIONf_dihedral_angle_d11.6174897
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.27531210.19272234X-RAY DIFFRACTION99.92
1.95-20.23651290.1662214X-RAY DIFFRACTION100
2-2.060.18821260.16282211X-RAY DIFFRACTION100
2.06-2.130.18111260.15572218X-RAY DIFFRACTION99.96
2.13-2.20.18391410.15172233X-RAY DIFFRACTION100
2.2-2.290.18931620.16262180X-RAY DIFFRACTION100
2.29-2.390.2061210.14952232X-RAY DIFFRACTION100
2.39-2.520.22161530.16872226X-RAY DIFFRACTION99.96
2.52-2.680.19321230.16132224X-RAY DIFFRACTION100
2.68-2.890.19231370.16652237X-RAY DIFFRACTION100
2.89-3.170.19461380.15682240X-RAY DIFFRACTION99.96
3.18-3.630.16761800.14562205X-RAY DIFFRACTION100
3.64-4.580.1391140.12152282X-RAY DIFFRACTION100
4.58-48.170.14521830.15792288X-RAY DIFFRACTION99.76
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)
11.73109147232-0.163223106119-0.06895010571061.984412622840.9811396474511.94707683683-0.03036340621190.1465425642510.00350050960699-0.2372472159530.0041684233146-0.0819215806387-0.02466201662420.1284919725660.02656905895770.168951150810.02103237536220.01558188357770.1480909936580.009493500155450.13476549361644.24625242532.917478124377.685269822
22.25015559763-0.7238153331140.3028012317152.244343878540.425138631240.9127203837720.00361884294111-0.0182047359766-0.1703679176130.0458743622083-0.04852748154360.2702180516320.0426150351536-0.1385774231150.04974179774660.1291849260890.008805721587660.006580418461880.149316373676-0.02504847706420.11384671379230.972497281132.819791441985.6308929046
30.3292595786420.04796885730940.3490717931131.540255094970.1854171943330.9408069302270.05033131868770.0881273626833-0.133411760649-0.230957498701-0.03089386227370.05780542809240.133170199975-0.00461168894034-0.01811098311150.232889334840.0275491074094-0.003659246919490.155463953162-0.04720049165920.19431594749742.17510605858.2505072455976.7393020356
41.045695569341.640646926450.3880222664574.90732452752-1.812662693353.303073866010.181912166711-0.1203619974730.01897453216380.4089330338110.04174002967530.09606526664180.150014848385-0.246862403622-0.2051508838810.2573291675040.00994221399033-0.03203040270420.181624645248-0.02315950603250.20465931354245.7441758633.1335161698491.0210711455
51.27257030965-1.208867956430.3281260416364.07660741398-0.5475937375260.7594932507050.04542502158740.0454569052193-0.05003684045540.0640820144005-0.0548643741801-0.2663360708850.06590612763380.1159350143980.02141904124530.141003197584-0.00170063333825-0.001179047437110.162560761494-0.04687493230550.16426900448350.334910870118.88367330686.3514616979
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 62 )3 - 621 - 60
22chain 'A' and (resid 63 through 141 )63 - 14161 - 133
33chain 'A' and (resid 142 through 234 )142 - 234134 - 226
44chain 'A' and (resid 235 through 278 )235 - 278227 - 257
55chain 'A' and (resid 279 through 328 )279 - 328258 - 307

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