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- PDB-3v4z: D-alanine--D-alanine ligase from Yersinia pestis -

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Basic information

Entry
Database: PDB / ID: 3v4z
TitleD-alanine--D-alanine ligase from Yersinia pestis
ComponentsD-alanine--D-alanine ligase
KeywordsLIGASE / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID / peptidoglycan synthesis
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, C-terminal / D-alanine--D-alanine ligase, N-terminal domain / D-ala D-ala ligase N-terminus / D-ala D-ala ligase C-terminus / D-alanine--D-alanine ligase signature 1. / D-alanine--D-alanine ligase signature 2. / 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, C-terminal / D-alanine--D-alanine ligase, N-terminal domain / D-ala D-ala ligase N-terminus / D-ala D-ala ligase C-terminus / D-alanine--D-alanine ligase signature 1. / D-alanine--D-alanine ligase signature 2. / 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / D-alanine--D-alanine ligase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsOsipiuk, J. / Nocek, B. / Mulligan, R. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: D-alanine--D-alanine ligase from Yersinia pestis.
Authors: Osipiuk, J. / Nocek, B. / Mulligan, R. / Papazisi, L. / Anderson, W.F. / Joachimiak, A.
History
DepositionDec 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
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 / 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 / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)67,1604
Polymers66,9042
Non-polymers2562
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-14 kcal/mol
Surface area25020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.637, 100.637, 110.304
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 33452.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: ddl, ddlB, y3624, YPO0557, YP_3627 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8ZIE7, D-alanine-D-alanine ligase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.41 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M magnesium chloride, 0.1 M sodium cacodylate, 50% PEG-200, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: SBC-3 / Detector: CCD / Date: Aug 13, 2008
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→31.6 Å / Num. all: 18282 / Num. obs: 18282 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Biso Wilson estimate: 70.5 Å2 / Rmerge(I) obs: 0.091 / Χ2: 1.142 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.7-2.7510.10.892.439070.68100
2.75-2.810.10.7949020.712100
2.8-2.8510.20.6478670.74100
2.85-2.9110.20.4989240.761100
2.91-2.9710.30.4418830.738100
2.97-3.0410.40.4699280.767100
3.04-3.1210.30.2598860.834100
3.12-3.210.30.2068900.883100
3.2-3.310.30.1649130.975100
3.3-3.410.30.1319121.11100
3.4-3.5210.30.1189001.062100
3.52-3.6610.30.1089171.13100
3.66-3.8310.10.0959151.29100
3.83-4.03100.089301.522100
4.03-4.299.90.0758851.555100
4.29-4.629.80.0679411.698100
4.62-5.089.70.0629151.639100
5.08-5.818.90.079371.778100
5.81-7.3280.0569381.6398.9
7.32-509.50.0389921.54298.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IOW

1iow


Resolution: 2.69→31.7 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.894 / WRfactor Rfree: 0.2552 / WRfactor Rwork: 0.1856 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7574 / SU B: 32.364 / SU ML: 0.305 / SU R Cruickshank DPI: 0.3159 / SU Rfree: 0.4021 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2888 927 5.1 %RANDOM
Rwork0.2053 ---
obs0.2094 18203 99.5 %-
all-18203 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.14 Å2 / Biso mean: 61.8005 Å2 / Biso min: 26.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.64 Å2-1.82 Å20 Å2
2---3.64 Å20 Å2
3---5.46 Å2
Refinement stepCycle: LAST / Resolution: 2.69→31.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4399 0 17 23 4439
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194497
X-RAY DIFFRACTIONr_angle_refined_deg1.8711.9856091
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4455575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15525.028181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.7315760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7481518
X-RAY DIFFRACTIONr_chiral_restr0.1090.2701
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213342
LS refinement shellResolution: 2.695→2.764 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.503 69 -
Rwork0.301 1141 -
all-1210 -
obs-1210 99.83 %
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)
10.8487-0.23650.07870.8480.60260.7556-0.02370.0282-0.1207-0.00350.08020.0703-0.00030.0026-0.05650.0059-0.01410.01490.0952-0.00740.08795.6619-27.9739-9.3727
21.1354-0.60530.02451.61721.28011.5455-0.05770.11840.2146-0.14170.0418-0.0666-0.18680.10520.01590.0711-0.02860.03020.2165-0.03230.15632.7133-35.2272-4.4591
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 306
2X-RAY DIFFRACTION2B1 - 306

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