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- PDB-4egq: Crystal structure of D-alanine-D-alanine ligase B from Burkholder... -

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Basic information

Entry
Database: PDB / ID: 4egq
TitleCrystal structure of D-alanine-D-alanine ligase B from Burkholderia pseudomallei
ComponentsD-alanine--D-alanine ligase
KeywordsLIGASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / flexible protein / ATP-dependent / magnesium dependent / cell wall biogenesis
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 / cytoplasm
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
D-alanine--D-alanine ligase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of D-alanine-D-alanine ligase B from Burkholderia pseudomallei
Authors: Edwards, T.E. / Fairman, J.W. / Abendroth, J. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionMar 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 13, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
C: D-alanine--D-alanine ligase
D: D-alanine--D-alanine ligase


Theoretical massNumber of molelcules
Total (without water)134,7094
Polymers134,7094
Non-polymers00
Water3,477193
1
A: D-alanine--D-alanine ligase


Theoretical massNumber of molelcules
Total (without water)33,6771
Polymers33,6771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: D-alanine--D-alanine ligase


Theoretical massNumber of molelcules
Total (without water)33,6771
Polymers33,6771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: D-alanine--D-alanine ligase


Theoretical massNumber of molelcules
Total (without water)33,6771
Polymers33,6771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: D-alanine--D-alanine ligase


Theoretical massNumber of molelcules
Total (without water)33,6771
Polymers33,6771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: D-alanine--D-alanine ligase

B: D-alanine--D-alanine ligase

C: D-alanine--D-alanine ligase
D: D-alanine--D-alanine ligase


Theoretical massNumber of molelcules
Total (without water)134,7094
Polymers134,7094
Non-polymers00
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation1_654x+1,y,z-11
crystal symmetry operation1_655x+1,y,z1
identity operation1_555x,y,z1
Buried area7310 Å2
ΔGint-57 kcal/mol
Surface area46920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.389, 66.092, 98.558
Angle α, β, γ (deg.)84.470, 80.500, 83.590
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 33677.227 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: BURPS1710b_3542, ddl / Production host: Escherichia coli (E. coli) / References: UniProt: Q3JNE1, D-alanine-D-alanine ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.14 Å3/Da / Density % sol: 42.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: BupsA.00119.a.A1 PW25270 at 30.8 mg/mL against Wizard Full screen condition D2, 1 M NaK Tartrate, 0.1 M CHES pH 9.5, 0.2 M Li2SO4, crystal tracking ID 203378d2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97946 Å
DetectorDate: Aug 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 54908 / % possible obs: 97.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.124 / Χ2: 1.001 / Net I/σ(I): 9.437
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.243.10.54627030.986196.6
2.24-2.283.20.51327441.094196.8
2.28-2.323.30.47426851.026197.2
2.32-2.373.40.43927480.951197.5
2.37-2.423.50.40427610.953197.7
2.42-2.483.60.37327310.923197.7
2.48-2.543.70.35127820.976197.9
2.54-2.613.80.31927430.965198
2.61-2.693.90.29827600.993198
2.69-2.773.90.23927171.004198
2.77-2.873.90.20927921.016198.3
2.87-2.993.90.18327561.048198.5
2.99-3.123.90.15627670.988198.5
3.12-3.293.90.13227910.977198.7
3.29-3.493.90.11627741.059198.7
3.49-3.763.90.10427830.988198.9
3.76-4.143.90.08927611.02199
4.14-4.743.80.07927440.984198.2
4.74-5.973.90.07527651.043198.2
5.97-503.80.08426011.025192.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å35.27 Å
Translation3 Å35.27 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4EG0

4eg0


Resolution: 2.2→35.27 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.909 / WRfactor Rfree: 0.262 / WRfactor Rwork: 0.2191 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.836 / SU B: 12.69 / SU ML: 0.157 / SU R Cruickshank DPI: 0.3313 / SU Rfree: 0.2304 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.331 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS NCS RESTRAINTS STATISTICS NCS TYPE: LOCAL NUMBER OF DIFFERENT NCS PAIRS: 6 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT ...Details: U VALUES: WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS NCS RESTRAINTS STATISTICS NCS TYPE: LOCAL NUMBER OF DIFFERENT NCS PAIRS: 6 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT 1 A 5 311 B 5 311 8225 0.09 0.05 2 A 4 311 C 4 311 7892 0.13 0.05 3 A 4 311 D 4 311 7741 0.11 0.05 4 B 5 310 C 5 310 8154 0.13 0.05 5 B 5 311 D 5 311 8071 0.12 0.05 6 C 4 311 D 4 311 7824 0.12 0.05
RfactorNum. reflection% reflectionSelection details
Rfree0.2503 2772 5.1 %RANDOM
Rwork0.2097 ---
obs0.2118 54818 97.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.76 Å2 / Biso mean: 38.9073 Å2 / Biso min: 17.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å2-0.04 Å21.48 Å2
2---0.69 Å20.59 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.2→35.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8399 0 0 193 8592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0198574
X-RAY DIFFRACTIONr_bond_other_d0.0070.025518
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.97611706
X-RAY DIFFRACTIONr_angle_other_deg1.411313436
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.39551169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.62222.895304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.126151141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4911553
X-RAY DIFFRACTIONr_chiral_restr0.0810.21360
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219901
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021792
LS refinement shellResolution: 2.2→2.261 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 171 -
Rwork0.246 3520 -
all-3691 -
obs--88.73 %
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)
10.66520.1367-0.02211.3006-0.05261.1073-0.05080.16420.098-0.26090.0551-0.0830.12490.1394-0.00430.0903-0.0430.01540.13350.0180.0234-1.71795.700375.2454
20.3763-0.033-0.04081.24970.20460.41390.0320.05340.0315-0.2223-0.0615-0.051-0.0114-0.04820.02960.05680.006-0.00910.02820.01420.0487-11.8287-27.631428.2687
30.65490.08120.35660.63480.09010.5921-0.03860.0113-0.04330.00920.0320.00660.13480.03930.00660.0844-0.0156-0.00240.0811-0.01810.062916.9188-9.21143.0765
40.49590.2078-0.0080.7595-0.07440.88410.0313-0.0767-0.01180.0448-0.01960.10160.10410.0648-0.01170.0497-0.02960.00030.0621-0.00320.027822.4922-47.789247.5769
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 311
2X-RAY DIFFRACTION2B5 - 312
3X-RAY DIFFRACTION3C4 - 311
4X-RAY DIFFRACTION4D4 - 311

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