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- PDB-3ue9: Crystal structure of Adenylosuccinate synthetase (AMPSase) (purA)... -

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Basic information

Entry
Database: PDB / ID: 3ue9
TitleCrystal structure of Adenylosuccinate synthetase (AMPSase) (purA) from Burkholderia thailandensis
ComponentsAdenylosuccinate synthetase
KeywordsLIGASE / SSGCID / AdSS / BTH_I2245 / IMP-aspartate ligase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


adenylosuccinate synthase / adenylosuccinate synthase activity / 'de novo' AMP biosynthetic process / GTP binding / magnesium ion binding / cytoplasm
Similarity search - Function
Adenylosuccinate Synthetase, subunit A; domain 2 / Adenylosuccinate Synthetase, subunit A, domain 2 / Adenylosuccinate Synthetase; Chain A, domain 1 / Adenylosuccinate Synthetase, subunit A, domain 1 / Adenylosuccinate Synthetase; Chain A, domain 3 / Adenylosuccinate Synthetase, subunit A, domain 3 / Adenylosuccinate synthase, active site / Adenylosuccinate synthetase active site. / Adenylosuccinate synthase, GTP-binding site / Adenylosuccinate synthetase, domain 2 ...Adenylosuccinate Synthetase, subunit A; domain 2 / Adenylosuccinate Synthetase, subunit A, domain 2 / Adenylosuccinate Synthetase; Chain A, domain 1 / Adenylosuccinate Synthetase, subunit A, domain 1 / Adenylosuccinate Synthetase; Chain A, domain 3 / Adenylosuccinate Synthetase, subunit A, domain 3 / Adenylosuccinate synthase, active site / Adenylosuccinate synthetase active site. / Adenylosuccinate synthase, GTP-binding site / Adenylosuccinate synthetase, domain 2 / Adenylosuccinate synthetase, domain 3 / Adenylosuccinate synthetase GTP-binding site. / Adenylosuccinate synthetase / Adenylosuccinate synthetase, domain 1 / Adenylosuccinate synthetase / Adenylosuccinate synthetase / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Adenylosuccinate synthetase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionOct 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenylosuccinate synthetase
B: Adenylosuccinate synthetase
C: Adenylosuccinate synthetase
D: Adenylosuccinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,80410
Polymers194,5604
Non-polymers2446
Water20,3211128
1
A: Adenylosuccinate synthetase
C: Adenylosuccinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,4025
Polymers97,2802
Non-polymers1223
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-32 kcal/mol
Surface area30240 Å2
MethodPISA
2
B: Adenylosuccinate synthetase
D: Adenylosuccinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,4025
Polymers97,2802
Non-polymers1223
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-29 kcal/mol
Surface area29490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.880, 74.590, 112.660
Angle α, β, γ (deg.)109.350, 90.010, 103.190
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Adenylosuccinate synthetase / AMPSase / AdSS / IMP--aspartate ligase


Mass: 48639.984 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: purA, BTH_I2245 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2SWD3, adenylosuccinate synthase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1128 / 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: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Internal tracking number 226144E11. JCSG screen condition E11: 14.4% PEG 8000 20% v/v glycerol 80 mM Cacodylate pH 6.5 160 mM Calcium acetate ButhA.00888.a.A1 PW33408 at 32.28 mg/ml., vapor ...Details: Internal tracking number 226144E11. JCSG screen condition E11: 14.4% PEG 8000 20% v/v glycerol 80 mM Cacodylate pH 6.5 160 mM Calcium acetate ButhA.00888.a.A1 PW33408 at 32.28 mg/ml., vapor diffusion, sitting drop, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 129329 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 23.361 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.95-23.770.442334114904790.8
2-2.060.3453.933990895392.6
2.06-2.120.2715.133960889894.3
2.12-2.180.2355.833487872995.1
2.18-2.250.2086.633706853995.8
2.25-2.330.1827.535032828796.4
2.33-2.420.1588.835567797196.8
2.42-2.520.1459.736069777597.1
2.52-2.630.12810.536302742397.3
2.63-2.760.1121236817718197.6
2.76-2.910.09713.837004677197.6
2.91-3.080.0915.936979641697.4
3.08-3.30.07420.138916606398.1
3.3-3.560.06127.241983566198
3.56-3.90.04934.137768518497.8
3.9-4.360.04535.433366460797.1
4.36-5.030.04237.629787413497.7
5.03-6.170.0532.526117353798.5
6.17-8.720.04435.519632269998.7
8.720.03544.410123145496.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å43.39 Å
Translation2.5 Å43.39 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HID

3hid


Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.904 / SU B: 7.803 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.247 6527 5 %RANDOM
Rwork0.201 ---
obs0.203 129328 96.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.263 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å20.86 Å20.36 Å2
2--2.38 Å20.59 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12667 0 12 1128 13807
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01913007
X-RAY DIFFRACTIONr_bond_other_d0.0010.028633
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.95917700
X-RAY DIFFRACTIONr_angle_other_deg0.89320915
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.64451708
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.70423.195579
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.775151971
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.04915117
X-RAY DIFFRACTIONr_chiral_restr0.0870.22002
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02114945
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022764
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 492 -
Rwork0.231 8545 -
all-9037 -
obs--90.82 %
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)
11.32910.4106-0.58810.9899-0.07410.2920.04820.10830.1815-0.0613-0.00610.1804-0.0716-0.0576-0.04210.11260.033-0.02810.05760.00480.1424-5.8727103.0859-3.6143
22.6254-0.17471.79880.91810.3191.7174-0.1233-0.15880.31410.0609-0.02540.1032-0.2037-0.15060.14870.09570.02730.04240.0289-0.03290.1459-9.827101.820710.5031
31.18970.06570.97970.49620.13732.1420.0362-0.2189-0.00440.1255-0.00780.10620.0942-0.1921-0.02830.06870.00480.02970.0485-0.01530.0999-9.569591.758816.8264
41.09570.5124-0.01770.7652-0.04830.39460.0370.0290.0255-0.03580.0230.0375-0.0379-0.0447-0.060.08040.02840.00130.0256-0.01140.08274.61898.2449-2.5481
51.00250.19570.15791.49970.00960.7420.0261-0.11270.14930.0748-0.0262-0.0494-0.168-0.055300.11780.02550.02590.0257-0.02880.104313.8613114.5336-0.8273
61.02390.09870.45590.7627-0.45071.57360.00250.10840.0593-0.02090.0121-0.076-0.05840.0218-0.01460.08820.02790.04920.0323-0.00530.09716.1443110.6887-11.9347
70.8303-0.08470.61780.25080.14261.30830.01010.128-0.0989-0.10810.0206-0.07330.02980.2209-0.03060.0769-0.0030.03580.1512-0.01750.095833.170657.529939.8975
81.85650.5822-0.97291.9096-1.03281.7095-0.08630.0393-0.313-0.08840.0277-0.16430.19380.07070.05850.02320.0095-0.00340.1265-0.00830.117737.993849.611650.7963
91.24260.3757-0.451.1648-0.94921.81380.0537-0.297-0.18420.1528-0.1101-0.1135-0.02450.26010.05640.0302-0.0013-0.01780.17310.04090.076737.350752.74562.4841
101.04530.5260.27291.05890.30950.57520.0428-0.06-0.0638-0.0102-0.0401-0.06680.00240.101-0.00270.0464-0.00630.00840.1070.0010.060223.105260.166443.5703
110.93120.0426-0.21021.21920.60111.59030.0148-0.0872-0.1971-0.0053-0.0768-0.03190.2157-0.01160.0620.07960.0091-0.01480.05720.00440.09813.60546.851834.1412
120.64880.2662-0.18480.8024-0.22121.99730.0415-0.0403-0.019-0.0701-0.04020.0463-0.0314-0.0864-0.00130.07090.0413-0.01980.047-0.03520.067411.49756.746928.6314
130.92530.3262-0.04691.03440.06740.0947-0.01250.0266-0.1235-0.04790.0082-0.14390.10340.02380.00440.1370.03290.01770.0249-0.0130.114815.373173.9996-0.8179
141.7147-0.1402-1.22430.7680.09232.2341-0.0563-0.2482-0.27210.0637-0.0615-0.06620.19590.16250.11780.07250.0182-0.01740.05220.04040.138720.508777.989711.6549
151.1783-0.0749-0.94850.69620.23612.90560.0437-0.23720.03460.1225-0.032-0.1447-0.12220.2644-0.01170.0639-0.0107-0.03240.05930.00540.070619.850989.124616.8388
161.09080.3818-0.62881.0641-0.47530.75810.019-0.02280.0367-0.00720.00750.01240.0380.0529-0.02650.07570.0165-0.0210.0271-0.02030.08235.327579.1446-0.6248
171.7254-0.11950.00181.577-0.74961.6643-0.0239-0.066-0.1966-0.03580.0610.10320.2094-0.1385-0.03710.1195-0.0037-0.01060.0279-0.0250.1235-3.534263.59034.6482
182.28770.5836-0.96671.5045-0.2042.0096-0.10430.4029-0.144-0.19680.17350.09060.2442-0.4278-0.06920.1323-0.0451-0.06740.1199-0.00650.0762-6.347165.2248-7.1173
190.66240.14780.35060.39890.19610.99120.0124-0.07080.08260.0381-0.0670.0669-0.1389-0.04510.05460.0530.00560.01150.1414-0.00530.070512.583377.285160.2749
202.357-1.74340.90411.8567-1.06452.211-0.0644-0.34310.02070.19730.04560.0802-0.0844-0.20190.01890.0425-0.04950.02850.2112-0.00340.05727.394466.169967.7611
210.9347-0.59170.84251.8933-1.07951.710.0717-0.1909-0.16410.0534-0.03960.2070.1679-0.2097-0.03210.0398-0.05920.01810.18750.03370.07427.904654.706164.2779
221.1101-0.13620.54260.26930.17371.2590.0274-0.0633-0.06260.00090.01890.048-0.0630.009-0.04630.0447-0.02550.01060.12540.01450.051222.409773.60657.3025
231.56410.0542-0.05971.05170.02921.5342-0.0251-0.24870.0620.0969-0.0104-0.0385-0.1930.24340.03540.0554-0.0430.00060.1337-0.02250.043631.312482.177771.2794
242.25-0.21310.99561.2965-0.31322.0584-0.09240.14890.3208-0.015-0.0493-0.1139-0.39540.39260.14170.1041-0.10740.00170.12770.00880.059233.98888.489861.1559
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 90
2X-RAY DIFFRACTION2A91 - 143
3X-RAY DIFFRACTION3A144 - 220
4X-RAY DIFFRACTION4A221 - 287
5X-RAY DIFFRACTION5A288 - 356
6X-RAY DIFFRACTION6A357 - 448
7X-RAY DIFFRACTION7B9 - 90
8X-RAY DIFFRACTION8B91 - 143
9X-RAY DIFFRACTION9B144 - 220
10X-RAY DIFFRACTION10B221 - 287
11X-RAY DIFFRACTION11B288 - 356
12X-RAY DIFFRACTION12B357 - 448
13X-RAY DIFFRACTION13C8 - 90
14X-RAY DIFFRACTION14C91 - 143
15X-RAY DIFFRACTION15C144 - 220
16X-RAY DIFFRACTION16C221 - 287
17X-RAY DIFFRACTION17C288 - 356
18X-RAY DIFFRACTION18C357 - 448
19X-RAY DIFFRACTION19D8 - 90
20X-RAY DIFFRACTION20D91 - 143
21X-RAY DIFFRACTION21D144 - 220
22X-RAY DIFFRACTION22D221 - 287
23X-RAY DIFFRACTION23D288 - 356
24X-RAY DIFFRACTION24D357 - 448

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