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- PDB-3vot: Crystal structure of L-amino acid ligase from Bacillus licheniformis -

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Basic information

Entry
Database: PDB / ID: 3vot
TitleCrystal structure of L-amino acid ligase from Bacillus licheniformis
ComponentsL-amino acid ligase, BL00235
KeywordsLIGASE / ATP-GRASP MOTIF / ATP-BINDING
Function / homology
Function and homology information


ATP binding / metal ion binding
Similarity search - Function
L-amino acid ligase, C-terminal domain 2 / BL00235/CARNS1, N-terminal / ATP-grasp N-terminal domain / L-amino acid ligase C-terminal domain 2 / ATP-grasp domain / Rossmann fold - #20 / ATP-grasp fold, B domain / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 ...L-amino acid ligase, C-terminal domain 2 / BL00235/CARNS1, N-terminal / ATP-grasp N-terminal domain / L-amino acid ligase C-terminal domain 2 / ATP-grasp domain / Rossmann fold - #20 / ATP-grasp fold, B domain / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ATP-grasp domain-containing protein
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsSuzuki, M. / Takahashi, Y. / Noguchi, A. / Arai, T. / Yagasaki, M. / Kino, K. / Saito, J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: The structure of L-amino-acid ligase from Bacillus licheniformis
Authors: Suzuki, M. / Takahashi, Y. / Noguchi, A. / Arai, T. / Yagasaki, M. / Kino, K. / Saito, J.
History
DepositionFeb 8, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.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_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: L-amino acid ligase, BL00235
B: L-amino acid ligase, BL00235
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,74016
Polymers95,2602
Non-polymers1,48014
Water11,385632
1
A: L-amino acid ligase, BL00235
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2938
Polymers47,6301
Non-polymers6637
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: L-amino acid ligase, BL00235
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4478
Polymers47,6301
Non-polymers8177
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.090, 90.030, 154.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein L-amino acid ligase, BL00235


Mass: 47629.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Strain: NBRC 12200 / DSM 13 / ATCC14580 / Gene: BL00235, BLi04240 / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q65D11, EC: 6.3.2.28

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Non-polymers , 5 types, 646 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 632 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Mosaicity (°)
12.1342.150.421
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
293.151vapor diffusion6.5100mM CaCl2, 24-27%(w/v) PEGMME 550, 4%(v/v) isopropanol in 100mM imidazole, pH 6.5, VAPOR DIFFUSION, temperature 293.15K
293.152vapor diffusion6.5100mM CaCl2, 24-27%(w/v) PEGMME 550, 4%(v/v) isopropanol in 100 mM imidazole, pH 6.5, VAPOR DIFFUSION, temperature 293.15K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06SA11
SYNCHROTRONSLS X06SA20.97920, 0.97970, 0.97200
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDSep 24, 2008
PSI PILATUS 6M2PIXELMay 9, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LN2 cooled fixed-exit, Si(111) monochromatorSINGLE WAVELENGTHMx-ray1
2LN2 cooled fixed-exit, Si(111) monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97921
30.97971
40.9721
Reflection
IDNumberRmerge(I) obsD res high (Å)Num. obs% possible obs
17241940.0691.2847359757.7
27045920.0531.2846577757
37364440.071.2748177557.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
2.713.824967289.210.05
2.212.71618308610.081
1.922.216942081.610.152
1.711.928230485.310.329
1.561.718726481.710.697
1.451.565699849.211.052
1.351.453073424.613.478
1.281.3586486.5115.831
2.713.835019290.520.036
2.212.715984883.420.062
1.922.216584077.620.137
1.721.928007683.220.259
1.571.728620080.920.593
1.451.575560248.121.132
1.361.453121625.121.896
1.281.3689726.823.251
2.693.85128790.330.043
2.22.696196284.330.082
1.92.26628476.230.208
1.71.98487286.130.484
1.551.78973082.230.988
1.441.555788148.832.273
1.351.443234725.439.462
1.271.3592396.8328.653
ReflectionResolution: 1.8→30.01 Å / Num. obs: 73218 / % possible obs: 96.37 % / Redundancy: 5.62 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 9.7066
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) allNum. measured allNum. unique allDiffraction-ID% possible all
1.8-1.95.490.645414598641,290.46
1.9-2.015.451.035201995441,291.92
2.01-2.155.411.575015692731,295.16
2.15-2.325.411.964826289221,297.84
2.32-2.555.533.394599383241,299.09
2.55-2.855.714.814330575851,299.43
2.85-3.295.877.193971767631,299.66
3.29-4.026.0710.443500757701,299.84
4.02-5.696.0813.082772545591,299.93
5.69-30.015.7112.291492426141,299.23

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MADD res high: 2.3 Å / D res low: 50 Å / FOM : 0.41 / Reflection: 36328
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
3 wavelength110.9724.62-2.27
3 wavelength120.97972.61-11.26
3 wavelength130.97926.09-9.51
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se29.3550.3240.1830.150.41
2Se14.4310.4940.2660.210.507
3Se20.6850.9960.9190.2030.493
4Se31.5960.1490.0020.1470.324
5Se15.1250.0130.9810.2010.344
6Se2.5060.4510.2050.2090.22
7Se4.7060.020.1420.150.21
8Se15.8280.4390.0440.1430.243
9Se9.0440.750.360.0950.195
10Se20.3470.7370.8260.0850.316
Phasing MAD shell
Resolution (Å)FOM Reflection
8.33-500.51792
5.24-8.330.543052
4.09-5.240.483847
3.47-4.090.474513
3.06-3.470.445097
2.77-3.060.415554
2.55-2.770.356051
2.37-2.550.296422
Phasing dmFOM : 0.6 / FOM acentric: 0.6 / FOM centric: 0.7 / Reflection: 98011 / Reflection acentric: 90752 / Reflection centric: 7259
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
4.6-48.640.960.960.95489238841008
2.9-4.60.940.940.9314336127341602
2.3-2.90.820.820.7917741163031438
2-2.30.680.680.6917105159961109
1.7-20.410.410.4228071266441427
1.6-1.70.210.210.211586615191675

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALACCP4_3.3.16data scaling
SOLVE2.13phasing
RESOLVE2.13phasing
REFMACrefmac_5.6.0117refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MAD / Resolution: 1.8→29.46 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.225 / WRfactor Rwork: 0.181 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.556 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2407 3625 5 %RANDOM
Rwork0.1959 ---
obs0.1981 73160 96.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 104.73 Å2 / Biso mean: 30.789 Å2 / Biso min: 10.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20 Å2
2---0.65 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6369 0 78 632 7079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196631
X-RAY DIFFRACTIONr_angle_refined_deg1.1591.9758992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3285813
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.524.29324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.587151114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7841542
X-RAY DIFFRACTIONr_chiral_restr0.0720.2985
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215084
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8470.3732150.3054504526489.647
1.847-1.8970.3052100.284374512089.531
1.897-1.9520.32320.2544270501089.86
1.952-2.0110.2852220.2354248485392.108
2.011-2.0770.2422360.2254150468093.718
2.077-2.150.2362320.2114073452795.096
2.15-2.230.2461830.2034028434097.028
2.23-2.3210.2452040.1923874417597.677
2.321-2.4230.2441770.1963735397998.316
2.423-2.5410.251980.1993553378499.128
2.541-2.6770.2481720.2063388359499.054
2.677-2.8380.2281640.1983198338299.409
2.838-3.0320.261630.1943000317599.622
3.032-3.2720.2141340.1842808296299.325
3.272-3.580.221580.1722540270499.778
3.58-3.9950.211140.1682305242799.67
3.995-4.5990.184940.1542033213199.812
4.599-5.5990.2341030.1711669177499.887
5.599-7.7780.267650.2111287135499.852
7.778-29.4620.252370.17468773099.178
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)
10.9969-0.097-0.23131.7557-0.430.8747-0.0104-0.20780.00220.2966-0.0124-0.08220.03180.08130.02290.0666-0.0016-0.01470.05170.00520.006355.898634.813857.8637
21.5732-0.37660.38712.08880.0990.5962-0.0794-0.2977-0.01490.38520.07920.0169-0.0372-0.02560.00030.0770.01070.00380.0633-0.00040.005232.163172.970555.7316
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 507
2X-RAY DIFFRACTION2B2 - 507

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