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- PDB-3q1k: The Crystal Structure of the D-alanyl-alanine Synthetase A from S... -

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Basic information

Entry
Database: PDB / ID: 3q1k
TitleThe Crystal Structure of the D-alanyl-alanine Synthetase A from Salmonella enterica Typhimurium Complexed with ADP
ComponentsD-alanine--D-alanine ligase A
KeywordsLIGASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha beta sandwich / cytosol
Function / homology
Function and homology information


D-alanine-D-alanine ligase / D-alanine-D-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / ATP binding / metal ion binding / cytosol
Similarity search - Function
D-alanine--D-alanine ligase/VANA/B/C, conserved site / D-alanine--D-alanine ligase / D-alanine--D-alanine ligase, N-terminal domain / D-ala D-ala ligase N-terminus / D-alanine--D-alanine ligase signature 1. / D-alanine--D-alanine ligase signature 2. / D-alanine--D-alanine ligase, C-terminal / D-ala D-ala ligase C-terminus / Rossmann fold - #20 / ATP-grasp fold, A domain ...D-alanine--D-alanine ligase/VANA/B/C, conserved site / D-alanine--D-alanine ligase / D-alanine--D-alanine ligase, N-terminal domain / D-ala D-ala ligase N-terminus / D-alanine--D-alanine ligase signature 1. / D-alanine--D-alanine ligase signature 2. / D-alanine--D-alanine ligase, C-terminal / D-ala D-ala ligase C-terminus / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / FORMIC ACID / D-alanine--D-alanine ligase A
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.202 Å
AuthorsZhang, R. / Maltseva, N. / Papazisi, L. / Anderson, W. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: The Crystal Structure of the D-alanyl-alanine Synthetase A from Salmonella enterica Typhimurium Complexed with ADP
Authors: Zhang, R. / Maltseva, N. / Papazisi, L. / Anderson, W. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
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_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.pdbx_leaving_atom_flag / _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
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-alanine--D-alanine ligase A
B: D-alanine--D-alanine ligase A
C: D-alanine--D-alanine ligase A
D: D-alanine--D-alanine ligase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,27321
Polymers159,7974
Non-polymers2,47617
Water8,665481
1
A: D-alanine--D-alanine ligase A
B: D-alanine--D-alanine ligase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,26613
Polymers79,8982
Non-polymers1,36711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7650 Å2
ΔGint-66 kcal/mol
Surface area27010 Å2
MethodPISA
2
C: D-alanine--D-alanine ligase A
D: D-alanine--D-alanine ligase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0078
Polymers79,8982
Non-polymers1,1096
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-42 kcal/mol
Surface area27460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.153, 85.813, 230.893
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
D-alanine--D-alanine ligase A / D-Ala-D-Ala ligase A / D-alanylalanine synthetase A


Mass: 39949.242 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: ddl, ddlA, STM0380 / Plasmid: pMCSG19c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic / References: UniProt: P0A1F0, D-alanine-D-alanine ligase

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Non-polymers , 6 types, 498 molecules

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


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 481 / 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: 2.64 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 8% PEG 4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2008 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 86501 / Num. obs: 86501 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Biso Wilson estimate: 39.41 Å2 / Rsym value: 0.088 / Net I/σ(I): 7.7
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 9 % / Mean I/σ(I) obs: 2.55 / Num. unique all: 4291 / Rsym value: 0.799 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 3I12

3i12


Resolution: 2.202→47.537 Å / SU ML: 0.32 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.221 4332 5.01 %random
Rwork0.176 ---
all0.178 86401 --
obs0.178 86401 99.89 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.048 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso mean: 47.1 Å2
Baniso -1Baniso -2Baniso -3
1--3.7684 Å2-0 Å20 Å2
2---0.3445 Å20 Å2
3---4.1129 Å2
Refinement stepCycle: LAST / Resolution: 2.202→47.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10634 0 155 481 11270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111080
X-RAY DIFFRACTIONf_angle_d1.27415084
X-RAY DIFFRACTIONf_chiral_restr0.0831758
X-RAY DIFFRACTIONf_plane_restr0.0061975
X-RAY DIFFRACTIONf_dihedral_angle_d17.7274036
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.2016-2.28030.2944400.22178009844999
2.2803-2.37160.27084310.205281298560100
2.3716-2.47950.25564240.189480928516100
2.4795-2.61020.25534650.186381028567100
2.6102-2.77370.26463980.186681968594100
2.7737-2.98790.27824120.197881658577100
2.9879-3.28850.25884360.199582318667100
3.2885-3.76420.21244120.184682438655100
3.7642-4.74180.17174610.137383138774100
4.7418-47.54780.19374530.167185899042100
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)
10.63080.2758-0.24230.7241-0.76091.093-0.0542-0.0045-0.069-0.07040.09710.05450.2053-0.0372-0.00220.2707-0.00920.0620.12890.00310.196544.011426.505449.0764
21.5030.11670.370.1737-0.08740.5381-0.08950.13490.2229-0.02240.06730.02690.03440.10240.04230.2105-0.02920.04690.1760.00320.21362.941643.648536.7297
30.74240.0557-0.57240.4704-0.1151.1184-0.0410.0593-0.133-0.0826-0.1190.06320.1731-0.10830.14740.22950.01610.02250.2337-0.04260.273292.27934.39142.7117
40.5320.4628-0.12720.5888-0.20490.53920.05510.06580.2103-0.017-0.1134-0.0024-0.01140.10430.0450.14790.02950.02060.2740.0740.3148108.422757.35035.5026
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA2 - 363
2X-RAY DIFFRACTION2chain BB2 - 363
3X-RAY DIFFRACTION3chain CC2 - 364
4X-RAY DIFFRACTION4chain DD3 - 363

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