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- PDB-2gu2: Crystal Structure of an Aspartoacylase from Rattus norvegicus -

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Basic information

Entry
Database: PDB / ID: 2gu2
TitleCrystal Structure of an Aspartoacylase from Rattus norvegicus
ComponentsAspa protein
KeywordsHYDROLASE / Aspartoacylase family / Aminoacylase-2 / ACY-2 / ACY2_RAT / Structural Genomics / PSI / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


Aspartate and asparagine metabolism / aspartoacylase / aspartoacylase activity / acetate metabolic process / aspartate metabolic process / central nervous system myelination / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / hydrolase activity, acting on ester bonds / positive regulation of oligodendrocyte differentiation / identical protein binding ...Aspartate and asparagine metabolism / aspartoacylase / aspartoacylase activity / acetate metabolic process / aspartate metabolic process / central nervous system myelination / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / hydrolase activity, acting on ester bonds / positive regulation of oligodendrocyte differentiation / identical protein binding / nucleus / metal ion binding / cytosol
Similarity search - Function
N-terminal domain of TfIIb - #160 / Aspartoacylase / : / Succinylglutamate desuccinylase/aspartoacylase / Succinylglutamate desuccinylase / Aspartoacylase family / N-terminal domain of TfIIb / Zn peptidases / Single Sheet / Aminopeptidase / 3-Layer(aba) Sandwich ...N-terminal domain of TfIIb - #160 / Aspartoacylase / : / Succinylglutamate desuccinylase/aspartoacylase / Succinylglutamate desuccinylase / Aspartoacylase family / N-terminal domain of TfIIb / Zn peptidases / Single Sheet / Aminopeptidase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.805 Å
AuthorsBitto, E. / Wesenberg, G.E. / Phillips Jr., G.N. / Bingman, C.A. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structure of aspartoacylase, the brain enzyme impaired in Canavan disease.
Authors: Bitto, E. / Bingman, C.A. / Wesenberg, G.E. / McCoy, J.G. / Phillips, G.N.
History
DepositionApr 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspa protein
B: Aspa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5569
Polymers70,9452
Non-polymers6117
Water9,944552
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-155 kcal/mol
Surface area25220 Å2
MethodPISA
2
A: Aspa protein
B: Aspa protein
hetero molecules

A: Aspa protein
B: Aspa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,11218
Polymers141,8904
Non-polymers1,22214
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area8950 Å2
ΔGint-327 kcal/mol
Surface area48660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.581, 135.778, 54.033
Angle α, β, γ (deg.)90.00, 101.49, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-744-

HOH

21A-755-

HOH

31B-776-

HOH

DetailsThe biological unit is likely a dimer with one biological unit in the asymmetric unit (chains A & B)

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Components

#1: Protein Aspa protein


Mass: 35472.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: BC078813, UNIPROT-Q9R1T5 / Plasmid: PVP 16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL834 P(RARE2) / References: UniProt: Q9R1T5, aspartoacylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, 0.005 MES PH 7.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (1.9 M Ammonium sulfate, 0.10 ...Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, 0.005 MES PH 7.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (1.9 M Ammonium sulfate, 0.10 M HEPPS PH 8.5). Crystal cryo-protected with well solution supplemented with a final concentration of 30% Ethylene glycol, temperature 293K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97928, 0.95373
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 19, 2006 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979281
20.953731
ReflectionResolution: 1.8→80 Å / Num. obs: 58208 / % possible obs: 97.5 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.093 / Χ2: 1.097 / Net I/σ(I): 9.949
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.8-1.844.20.472.16734240.76686.6
1.84-1.894.90.4437010.78493.9
1.89-1.945.90.3838850.82497
1.94-26.70.34239100.85697.7
2-2.067.30.29338650.94997.9
2.06-2.137.60.2338820.97698.1
2.13-2.227.60.19139111.08398.3
2.22-2.327.60.16739081.16898.5
2.32-2.447.60.14239381.20598.7
2.44-2.67.60.12439091.22298.8
2.6-2.87.60.10239401.27198.9
2.8-3.087.70.08739441.29599.2
3.08-3.527.60.0739641.26299.3
3.52-4.447.60.05740011.13399.6
4.44-807.50.0640261.20899.7

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Phasing

PhasingMethod: MAD
Phasing MAD set

Highest resolution: 2.4 Å / Lowest resolution: 40.5 Å

IDR cullis acentricR cullis centricPower acentricPower centricReflection acentricReflection centric
ISO_1000024757617
ISO_20.6350.7021.9851.48224741617
ANO_10.61601.8990247340
ANO_20.79300.760247340
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricPower acentricPower centricReflection acentricReflection centric
ISO_110.39-40.5000028636
ISO_17.47-10.39000050933
ISO_16.14-7.47000065828
ISO_15.33-6.14000078533
ISO_14.77-5.33000089035
ISO_14.36-4.77000097828
ISO_14.04-4.360000104932
ISO_13.78-4.040000114530
ISO_13.57-3.780000119129
ISO_13.39-3.570000128829
ISO_13.23-3.390000135334
ISO_13.09-3.230000140830
ISO_12.97-3.090000145433
ISO_12.87-2.970000153526
ISO_12.77-2.870000159628
ISO_12.68-2.770000162733
ISO_12.6-2.680000166627
ISO_12.53-2.60000173032
ISO_12.46-2.530000176625
ISO_12.4-2.460000184336
ANO_110.39-40.50.51102.11502840
ANO_17.47-10.390.55102.14305070
ANO_16.14-7.470.53202.38806580
ANO_15.33-6.140.54602.25307840
ANO_14.77-5.330.59702.06308870
ANO_14.36-4.770.64901.83609780
ANO_14.04-4.360.61601.925010490
ANO_13.78-4.040.62101.981011450
ANO_13.57-3.780.64801.909011900
ANO_13.39-3.570.60602.01012870
ANO_13.23-3.390.59602.092013520
ANO_13.09-3.230.60802.018014080
ANO_12.97-3.090.58401.996014540
ANO_12.87-2.970.60301.959015320
ANO_12.77-2.870.61401.848015950
ANO_12.68-2.770.61301.818016260
ANO_12.6-2.680.65901.642016660
ANO_12.53-2.60.68301.56017290
ANO_12.46-2.530.70401.413017630
ANO_12.4-2.460.73301.304018400
ISO_210.39-40.50.5240.7032.4591.49928636
ISO_27.47-10.390.5610.7592.3971.71250933
ISO_26.14-7.470.540.5362.6232.04165828
ISO_25.33-6.140.5850.6412.5161.98278533
ISO_24.77-5.330.6240.6442.2171.82689035
ISO_24.36-4.770.6650.6522.011.61597828
ISO_24.04-4.360.6460.5651.9681.655104932
ISO_23.78-4.040.6280.681.9321.642114530
ISO_23.57-3.780.6360.8141.941.29119129
ISO_23.39-3.570.6190.71.9691.329128829
ISO_23.23-3.390.6261.0581.9791.269135334
ISO_23.09-3.230.6450.6491.9851.481140830
ISO_22.97-3.090.6530.8061.9741.064145433
ISO_22.87-2.970.6440.7961.9781.234153526
ISO_22.77-2.870.6480.7171.8920.946159628
ISO_22.68-2.770.6720.7991.8541.303162733
ISO_22.6-2.680.6650.7441.7661.109166627
ISO_22.53-2.60.6660.5941.6581.324173032
ISO_22.46-2.530.681.0361.5371.065176625
ISO_22.4-2.460.7050.7941.4560.927182736
ANO_210.39-40.50.68800.8702850
ANO_27.47-10.390.7100.89805070
ANO_26.14-7.470.67101.09606580
ANO_25.33-6.140.70200.97407840
ANO_24.77-5.330.71800.94608890
ANO_24.36-4.770.75500.84909780
ANO_24.04-4.360.75400.866010490
ANO_23.78-4.040.7700.866011450
ANO_23.57-3.780.78300.859011910
ANO_23.39-3.570.75600.862012880
ANO_23.23-3.390.77500.828013530
ANO_23.09-3.230.78900.806014080
ANO_22.97-3.090.79200.744014540
ANO_22.87-2.970.80800.733015350
ANO_22.77-2.870.82400.671015950
ANO_22.68-2.770.83700.632016270
ANO_22.6-2.680.86200.607016650
ANO_22.53-2.60.88300.559017300
ANO_22.46-2.530.89800.489017660
ANO_22.4-2.460.91100.462018270
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
112.205-5.83824.003SE17.541.02
231.29130.9250.296SE21.320.95
36.617-2.08224.053SE20.10.98
410.1647.07419.77SE16.370.89
528.0844.0483.554SE190.84
62.484-1.23120.616SE40.611.11
730.06639.38717.015SE29.180.91
838.61739.973.465SE21.30.83
946.346-30.5342.189SE29.580.96
1076.85-1.49417.262SE29.960.68
Phasing dmFOM : 0.57 / FOM acentric: 0.57 / FOM centric: 0.61 / Reflection: 58207 / Reflection acentric: 57196 / Reflection centric: 1011
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.2-41.7520.960.960.9426032465138
3.2-5.20.940.950.8679557744211
2.6-3.20.850.850.7699029721181
2.3-2.60.650.650.5599819821160
1.9-2.30.380.380.311763117404227
1.8-1.90.150.150.15101351004194

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RESOLVE2.06phasing
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
SHELXEmodel building
ARP/wARPmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.805→41.75 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.194 / WRfactor Rwork: 0.15 / SU B: 4.361 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.194 2955 5.077 %Random
Rwork0.1494 ---
all0.152 ---
obs-58208 97.248 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.762 Å2
Baniso -1Baniso -2Baniso -3
1-0.168 Å20 Å20.118 Å2
2--0.098 Å20 Å2
3----0.219 Å2
Refinement stepCycle: LAST / Resolution: 1.805→41.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4862 0 27 552 5441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0225081
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.976910
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8455634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80624.335233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.56115876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5251527
X-RAY DIFFRACTIONr_chiral_restr0.1240.2757
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023871
X-RAY DIFFRACTIONr_nbd_refined0.2080.22473
X-RAY DIFFRACTIONr_nbtor_refined0.3110.23498
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2423
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.237
X-RAY DIFFRACTIONr_mcbond_it1.86823216
X-RAY DIFFRACTIONr_mcangle_it2.99245071
X-RAY DIFFRACTIONr_scbond_it5.09862110
X-RAY DIFFRACTIONr_scangle_it7.02481831
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)
1.805-1.8520.2681930.20835230.211441484.187
1.852-1.9030.251950.18738570.19429794.298
1.903-1.9580.2151880.15938820.162418697.229
1.958-2.0180.2222020.14837660.152406197.71
2.018-2.0840.1721920.14236750.143394498.048
2.084-2.1570.1811760.13735910.139384198.073
2.157-2.2390.1681950.13833960.14365298.33
2.239-2.330.21920.14132860.145353198.499
2.33-2.4340.2051570.14531920.147339598.645
2.434-2.5520.211510.15530640.158325598.771
2.552-2.690.2061780.14928710.153308398.897
2.69-2.8530.21550.1527600.153294499.015
2.853-3.050.1851330.15525980.157275399.201
3.05-3.2940.2141310.14724090.15256099.219
3.294-3.6070.1661280.13922210.141236199.492
3.607-4.0320.1941080.13220160.134213499.531
4.032-4.6530.154970.13117930.132189699.684
4.653-5.6940.165780.14914990.15158199.747
5.694-8.0290.229660.1911890.192125799.841
8.029-75.3780.229400.1866650.18871099.296
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)
10.886-0.0988-0.20490.84350.33750.6662-0.04390.0717-0.0577-0.15190.082-0.0151-0.1135-0.0156-0.0381-0.021-0.03480.0098-0.029-0.0263-0.043921.13441.232-1.392
21.4881-0.43310.26840.23230.21560.8607-0.0170.0488-0.1797-0.02280.02030.0458-0.0147-0.1688-0.0033-0.0525-0.0230.0022-0.0197-0.00680.01136.62933.8342.071
30.2746-0.01280.02240.57640.33680.6623-0.0348-0.0014-0.0990.02780.0315-0.04850.01330.05310.0032-0.0627-0.00970.0145-0.0411-0.02070.00429.2335.37513.316
40.6440.26910.00181.43110.83440.7766-0.010.01890.02580.1478-0.09470.24690.0438-0.15420.1047-0.01580.00770.0207-0.0336-0.0196-0.031714.9465.14430.743
50.94730.3292-0.88663.92681.93493.37030.01730.16720.1069-0.2799-0.3210.8938-0.4172-0.7820.3036-0.06640.1285-0.10430.105-0.06720.18053.05573.05122.113
60.29990.1287-0.14550.77730.48370.6607-0.04620.04680.0533-0.04080.04560.0236-0.0957-0.010.0005-0.013-0.0008-0.0236-0.04820.0029-0.049128.50770.57320.465
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA4 - 704 - 70
22AA71 - 10571 - 105
33AA106 - 310106 - 310
44BB4 - 704 - 70
55BB71 - 10571 - 105
66BB106 - 310106 - 310

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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