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- PDB-4iv5: X-ray crystal structure of a putative aspartate carbamoyltransfer... -

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Basic information

Entry
Database: PDB / ID: 4iv5
TitleX-ray crystal structure of a putative aspartate carbamoyltransferase from Trypanosoma cruzi
ComponentsAspartate carbamoyltransferase, putative
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / aspartate carbamoyltransferase
Function / homology
Function and homology information


aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / cellular amino acid metabolic process / amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process
Similarity search - Function
Aspartate carbamoyltransferase / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / Aspartate/ornithine carbamoyltransferase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Aspartate carbamoyltransferase / Aspartate carbamoyltransferase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: X-ray crystal structure of a putative aspartate carbamoyltransferase from Trypanosoma cruzi
Authors: Fairman, J.W. / Abendroth, J.A. / Edwards, T.E. / Lorimer, D.
History
DepositionJan 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartate carbamoyltransferase, putative
B: Aspartate carbamoyltransferase, putative
C: Aspartate carbamoyltransferase, putative
D: Aspartate carbamoyltransferase, putative
E: Aspartate carbamoyltransferase, putative
F: Aspartate carbamoyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,78724
Polymers222,1556
Non-polymers63218
Water15,637868
1
A: Aspartate carbamoyltransferase, putative
B: Aspartate carbamoyltransferase, putative
F: Aspartate carbamoyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,36211
Polymers111,0783
Non-polymers2858
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-46 kcal/mol
Surface area31460 Å2
MethodPISA
2
C: Aspartate carbamoyltransferase, putative
D: Aspartate carbamoyltransferase, putative
E: Aspartate carbamoyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,42513
Polymers111,0783
Non-polymers34710
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6480 Å2
ΔGint-46 kcal/mol
Surface area31500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.980, 134.550, 159.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Aspartate carbamoyltransferase, putative /


Mass: 37025.840 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: CL Brener / Gene: Tc00.1047053508375.30, Tc00.1047053511923.110 / Production host: Escherichia coli (E. coli)
References: UniProt: O15636, UniProt: Q4D3W3*PLUS, aspartate carbamoyltransferase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 11 / Source method: obtained synthetically
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 868 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: pACT E10: 0.2 M sodium monobasic phosphate/potassium dibasic phosphate, 20% PEG 3350, protein at 18.47 mg/ml K, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 105706 / Num. obs: 102675 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.127 / Net I/σ(I): 8.93
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.1-2.150.5552.61191.8
2.15-2.210.4963.06198.7
2.21-2.280.4523.34199.2
2.28-2.350.3773.97199.3
2.35-2.420.3684.03199.1
2.42-2.510.3034.77198.8
2.51-2.60.2645.24198.8
2.6-2.710.2335.83198.5
2.71-2.830.2036.29198.4
2.83-2.970.1766.83198
2.97-3.130.1468197.8
3.13-3.320.1159.98197.6
3.32-3.550.08214.35197
3.55-3.830.06318.83196.4
3.83-4.20.05322.27195.8
4.2-4.70.04625.03195.3
4.7-5.420.05221.81194.2
5.42-6.640.06516.78193.7
6.64-9.390.04322.05191.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ML4
Resolution: 2.1→49.48 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 10.118 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23807 5134 5 %RANDOM
Rwork0.19146 ---
obs0.19381 97768 97.17 %-
all-105706 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.475 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å20 Å20 Å2
2---0.23 Å2-0 Å2
3---1.39 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13462 0 45 868 14375
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01913756
X-RAY DIFFRACTIONr_bond_other_d0.0010.0213442
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.97418670
X-RAY DIFFRACTIONr_angle_other_deg0.808330771
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.21951781
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.21423.189533
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.523152355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.85715105
X-RAY DIFFRACTIONr_chiral_restr0.0760.22258
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02115384
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023005
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6011.1717118
X-RAY DIFFRACTIONr_mcbond_other0.6011.1717117
X-RAY DIFFRACTIONr_mcangle_it1.0041.7528874
X-RAY DIFFRACTIONr_scbond_it0.6821.2236638
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 326 -
Rwork0.241 6712 -
obs--91.33 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.9562.40934.23482.87442.850810.71160.06140.30780.42580.17050.15930.2454-0.4189-0.2823-0.22070.09740.05560.06250.16630.11120.207843.0242119.09369.1208
21.5299-0.1556-0.30111.28730.01660.82860.05940.1430.0981-0.0191-0.06790.0222-0.0578-0.01890.00850.0459-0.00010.01620.05780.01520.015347.0194109.125712.9503
33.4449-1.268-2.70647.00162.36489.1203-0.443-0.8150.34710.79310.3744-0.07870.38620.53350.06860.2680.034-0.09090.3499-0.11120.417765.6404114.887528.2163
42.67480.29770.23042.0026-0.26812.42380.1532-0.23040.5590.2509-0.0513-0.0393-0.2964-0.0245-0.10190.0754-0.00840.030.0272-0.05540.145855.4662121.084924.5922
51.83280.072-0.43531.6336-0.55490.58990.0002-0.02650.15770.12770.02320.1842-0.0788-0.1266-0.02340.0794-0.00140.03330.1011-0.0160.071535.6626111.062723.4194
63.0976-1.27280.05665.4816-1.58513.257-0.0514-0.23020.28960.5979-0.02170.6409-0.1077-0.05750.07310.18130.02090.16870.1372-0.0410.232625.4078112.722533.3233
71.87410.1781-0.33921.6029-0.62241.3724-0.019-0.0615-0.11090.16690.01120.2250.0227-0.15580.00780.0683-0.02030.05340.0542-0.01620.058734.628298.320824.616
81.2455-1.8521-2.87685.43490.395117.02290.27250.0695-0.1366-0.3992-0.3798-0.0809-0.09730.48420.10730.1846-0.0173-0.0150.1435-0.07080.223859.772382.59872.8773
92.98651.9234-0.85574.3692-2.66273.6942-0.05020.1909-0.4508-0.16730.0065-0.14210.31010.14830.04370.0755-0.00490.03760.1016-0.07960.115369.141183.5644.4952
103.1339-0.83492.16191.87180.231812.7899-0.0540.054-0.01390.16180.00710.02240.18370.18280.04690.0356-0.0090.02110.0105-0.00690.051859.391394.798114.1715
112.015-0.2563-0.84960.95070.161.079-0.1126-0.0975-0.24770.1813-0.0042-0.01110.1260.03810.11680.0521-0.01030.01210.03010.00580.035159.585490.38620.3024
124.24660.5809-0.29344.64491.41625.44660.0067-0.258-0.67930.4442-0.2831-0.40830.52950.01920.27640.130.0250.05130.07150.10070.264678.27972.862716.4475
133.66383.64590.55257.70571.13312.34360.5281-0.7181-0.60821.0455-0.6202-1.21820.52620.01340.09210.2979-0.0016-0.08680.21520.18330.36887.065477.389521.5837
145.76950.47331.22862.2535-0.01831.71960.0334-0.1315-0.35590.1258-0.1551-0.45750.0920.20530.12180.07220.01340.01890.11160.02160.178681.28786.156514.911
153.69941.37440.90923.84431.38630.55530.0654-0.1659-0.33150.27390.0181-0.18760.0987-0.0064-0.08350.1330.01810.03780.06020.08320.216563.131580.740371.3626
162.02160.19170.13171.43390.33710.8817-0.0794-0.0865-0.16560.05870.02760.070.03330.03430.05180.0305-0.00770.0180.0250.00720.022757.257192.153970.7074
171.23770.454-0.2271.6797-0.10.1532-0.10070.3705-0.0903-0.181-0.0233-0.01930.0075-0.10880.1240.1077-0.00110.02710.177-0.05710.113370.059892.099654.9208
181.87870.85820.73441.42670.29340.9175-0.08960.1666-0.4622-0.01940.0625-0.01170.0652-0.02150.02710.059-0.01380.0690.0456-0.07270.227151.104575.44459.8782
1916.3795-0.12694.88068.0186-0.23649.7948-0.1805-0.2648-0.19580.305-0.01310.08050.22080.45480.19360.1936-0.01940.08490.0754-0.08710.331848.848261.64261.9886
203.1786-0.0051-0.51623.18790.26064.49570.00630.3915-0.5419-0.1153-0.17630.3650.0541-0.32290.170.0317-0.01930.04140.1031-0.16220.301537.811774.755.378
212.37070.52950.42581.25080.35871.3247-0.08870.0713-0.2217-0.0139-0.09130.30510.0778-0.08350.180.054-0.01250.03590.0404-0.05730.155141.624885.847163.278
221.3057-0.73010.06591.66610.23881.0420.0172-0.10240.08490.09190.03830.1065-0.0792-0.0025-0.05550.09440.00530.03170.05250.00060.036249.1678117.554870.6386
230.38790.09650.42411.85620.52832.1184-0.03170.0778-0.0304-0.2064-0.04590.2802-0.0597-0.09580.07760.06530.0102-0.02380.0469-0.01680.050545.0475103.337559.2435
240.5645-0.12790.03782.0105-0.86980.79550.09020.06770.0978-0.0712-0.02070.2432-0.0329-0.0005-0.06950.0650.03640.00920.03750.01130.057540.6694128.690558.9021
252.2905-0.9948-1.07814.11550.89283.9042-0.1670.1659-0.10550.15710.15980.53950.0798-0.3450.00720.05740.03310.01280.09190.0490.228.6761134.053558.6928
262.51380.7583-0.3333.0941-0.50680.90070.04210.37580.266-0.4164-0.00880.085-0.1290.0665-0.03330.16110.04740.00350.1280.07030.086745.1659138.314149.4965
274.2286-4.9834-8.74398.93596.705925.47960.28090.06080.4411-0.2984-0.1678-0.1567-0.45130.2078-0.11310.1466-0.00060.0570.16690.06440.558453.0732145.915353.9285
281.29920.2571-0.27141.915-0.8051.39150.07680.08930.1863-0.0327-0.07160.03080.03810.1152-0.00520.04470.03180.01350.0540.01390.028153.8647128.397461.2878
292.2967-0.95240.18821.3285-0.29241.81840.0372-0.09220.29920.0013-0.0055-0.3961-0.1070.1157-0.03170.1003-0.01790.01660.0812-0.03860.141686.0784117.405967.905
3010.84777.3562-6.63495.0959-4.57354.15380.3027-0.76370.1470.1729-0.30030.046-0.06870.3574-0.00240.2167-0.0135-0.00220.3756-0.07920.089281.764103.161175.0099
312.4153-1.3826-0.55333.22410.05480.2245-0.01530.1012-0.0409-0.1595-0.03790.0310.0494-0.07710.05320.0417-0.00360.01580.0994-0.01320.038170.0425109.376563.5332
321.9373-1.3883-0.36111.46080.84620.80820.42080.51640.151-0.3338-0.3807-0.1166-0.118-0.1142-0.04020.22670.09930.04310.2140.05660.097567.5461119.849955.1202
332.2152-0.7157-1.1991.93611.12121.24060.1420.08180.2175-0.1923-0.0057-0.372-0.19650.0551-0.13630.1168-0.00080.05520.08950.04390.136188.7408111.733555.5931
343.8857-1.321-0.84634.8811.45954.07370.21990.24870.5907-0.6202-0.0103-0.7903-0.40880.0917-0.20960.2201-0.03480.22110.13460.03220.291899.4612112.188346.4169
351.6485-0.5573-0.86712.00590.81052.006-0.09210.0096-0.1236-0.1678-0.016-0.27810.13830.1030.10820.07440.01760.06210.05360.02240.081588.503398.402955.2168
3618.3582-9.4343-6.533510.69621.64722.83830.4680.89550.2749-1.0436-0.3784-0.48650.0273-0.371-0.08960.2491-0.05740.14530.23130.08910.342381.1612116.3776-0.2907
373.57011.45490.22250.67360.11340.4188-0.02950.33660.1552-0.03940.1561-0.1053-0.27050.1074-0.12650.1826-0.04450.12020.15910.00670.397680.8449122.78445.9712
3813.7415-10.5005-6.043120.26316.510215.55390.05680.4740.478-0.48990.1495-0.5362-0.11120.1595-0.20630.1941-0.02410.10110.25950.12780.139662.8529118.78180.3798
393.4951-1.3403-0.42814.99711.59110.72390.0193-0.15990.2370.10190.0433-0.3015-0.02060.0443-0.06260.0521-0.03610.04020.0639-0.0260.116870.5065110.5214.1255
4025.592-2.3379-0.14250.21930.01460.0043-0.1273-0.06960.07910.06270.0717-0.00820.0231-0.02810.05560.47380.0413-0.08990.6101-0.03840.400577.962999.156423.7753
411.43340.54860.18131.02340.56170.37950.0357-0.15360.10520.35670.0564-0.24750.16160.129-0.09210.2545-0.0167-0.10440.247-0.01540.306980.8631104.354919.2992
420.15390.46970.06891.6459-0.02290.5260.0001-0.0027-0.02990.1126-0.0244-0.1788-0.1080.10840.02430.0819-0.0340.01840.0983-0.02070.225679.7608129.956719.3708
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 15
2X-RAY DIFFRACTION2A16 - 81
3X-RAY DIFFRACTION3A82 - 94
4X-RAY DIFFRACTION4A95 - 126
5X-RAY DIFFRACTION5A127 - 189
6X-RAY DIFFRACTION6A190 - 227
7X-RAY DIFFRACTION7A228 - 327
8X-RAY DIFFRACTION8B3 - 14
9X-RAY DIFFRACTION9B15 - 46
10X-RAY DIFFRACTION10B47 - 60
11X-RAY DIFFRACTION11B61 - 151
12X-RAY DIFFRACTION12B152 - 194
13X-RAY DIFFRACTION13B195 - 272
14X-RAY DIFFRACTION14B273 - 327
15X-RAY DIFFRACTION15C3 - 21
16X-RAY DIFFRACTION16C22 - 81
17X-RAY DIFFRACTION17C82 - 127
18X-RAY DIFFRACTION18C128 - 211
19X-RAY DIFFRACTION19C212 - 222
20X-RAY DIFFRACTION20C223 - 268
21X-RAY DIFFRACTION21C269 - 327
22X-RAY DIFFRACTION22D4 - 75
23X-RAY DIFFRACTION23D76 - 128
24X-RAY DIFFRACTION24D129 - 204
25X-RAY DIFFRACTION25D205 - 222
26X-RAY DIFFRACTION26D223 - 271
27X-RAY DIFFRACTION27D272 - 282
28X-RAY DIFFRACTION28D283 - 327
29X-RAY DIFFRACTION29E3 - 28
30X-RAY DIFFRACTION30E29 - 46
31X-RAY DIFFRACTION31E47 - 81
32X-RAY DIFFRACTION32E82 - 120
33X-RAY DIFFRACTION33E121 - 196
34X-RAY DIFFRACTION34E197 - 230
35X-RAY DIFFRACTION35E231 - 327
36X-RAY DIFFRACTION36F4 - 11
37X-RAY DIFFRACTION37F12 - 38
38X-RAY DIFFRACTION38F39 - 47
39X-RAY DIFFRACTION39F48 - 81
40X-RAY DIFFRACTION40F82 - 97
41X-RAY DIFFRACTION41F98 - 120
42X-RAY DIFFRACTION42F121 - 327

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