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- PDB-7u56: Crystal Structure of D-alanine--D-alanine ligase from Klebsiella ... -

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Basic information

Entry
Database: PDB / ID: 7u56
TitleCrystal Structure of D-alanine--D-alanine ligase from Klebsiella pneumoniae subsp. pneumoniae in complex with AMP
ComponentsD-alanine--D-alanine ligase
KeywordsLIGASE / SSGCID / cell wall formation / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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. / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily ...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. / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile.
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / D-alanine--D-alanine ligase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
CitationJournal: to be published
Title: Crystal Structure of D-alanine--D-alanine ligase from Klebsiella pneumoniae subsp. pneumoniae in complex with AMP
Authors: Abendroth, J. / Bolejack, M.J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionMar 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)85,16918
Polymers83,7882
Non-polymers1,38116
Water13,583754
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint-69 kcal/mol
Surface area26340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.350, 115.420, 68.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-548-

HOH

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 41893.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria)
Strain: HS11286 / Gene: ddl, KPHS_10610 / Plasmid: KlpnC.00137.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3GSI5, D-alanine-D-alanine ligase

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Non-polymers , 5 types, 770 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 754 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.25 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Anatrace/Calibre MCSG1 screen, condition B11: 200mM magnesium chloride, 100mM TrisBase / HCl pH 8.5, 20% (w/V) PEG 8000: KlpnC.00137.a.B1.PW38983 at 17mg/ml + 3mM Magensium chloride + 3mM ...Details: Anatrace/Calibre MCSG1 screen, condition B11: 200mM magnesium chloride, 100mM TrisBase / HCl pH 8.5, 20% (w/V) PEG 8000: KlpnC.00137.a.B1.PW38983 at 17mg/ml + 3mM Magensium chloride + 3mM AMP: tray: 322140 B11: cryo: 20% EG, puck: ody5-7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 10, 2022 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 65184 / % possible obs: 100 % / Redundancy: 6.136 % / Biso Wilson estimate: 27.571 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.088 / Χ2: 0.905 / Net I/σ(I): 16.16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.85-1.96.1330.6462.7447500.8150.706100
1.9-1.956.1710.4893.6546430.8890.534100
1.95-2.016.1790.3984.4745270.9240.434100
2.01-2.076.1830.3185.6443740.9460.347100
2.07-2.146.1860.2527.0142870.9670.275100
2.14-2.216.190.2048.6441070.9790.223100
2.21-2.296.1930.1799.7339700.9840.196100
2.29-2.396.1890.13912.2638440.990.152100
2.39-2.496.1940.12113.8936940.9920.132100
2.49-2.626.2010.10815.3135380.9940.118100
2.62-2.766.1780.08718.633450.9950.095100
2.76-2.936.1720.07221.8231890.9970.079100
2.93-3.136.1380.06225.1230200.9970.067100
3.13-3.386.1350.05129.1428090.9980.056100
3.38-3.76.0850.04334.4225910.9990.047100
3.7-4.146.0470.03737.8823570.9990.041100
4.14-4.786.0320.03541.6120940.9990.038100
4.78-5.855.9570.03640.518030.9990.03999.9
5.85-8.275.7990.03740.7914170.9980.041100
8.27-505.2180.03543.648250.9980.03998.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.20.1refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3i12 as per Morda

3i12


Resolution: 1.85→39.13 Å / SU ML: 0.1947 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.9761
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1992 1967 3.02 %0
Rwork0.1617 63212 --
obs0.1628 65179 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.92 Å2
Refinement stepCycle: LAST / Resolution: 1.85→39.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5119 0 84 755 5958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00795316
X-RAY DIFFRACTIONf_angle_d0.88687229
X-RAY DIFFRACTIONf_chiral_restr0.0618862
X-RAY DIFFRACTIONf_plane_restr0.0079967
X-RAY DIFFRACTIONf_dihedral_angle_d13.30411945
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.27871260.23154476X-RAY DIFFRACTION100
1.9-1.950.2361530.20024425X-RAY DIFFRACTION99.98
1.95-20.20831210.18124465X-RAY DIFFRACTION100
2-2.070.2261400.16654460X-RAY DIFFRACTION100
2.07-2.140.19791500.16484473X-RAY DIFFRACTION99.98
2.14-2.230.21851500.16744466X-RAY DIFFRACTION100
2.23-2.330.23121450.16264461X-RAY DIFFRACTION100
2.33-2.450.21431540.15794514X-RAY DIFFRACTION100
2.45-2.610.19051210.16314476X-RAY DIFFRACTION100
2.61-2.810.20821360.16444532X-RAY DIFFRACTION99.98
2.81-3.090.20071330.1654542X-RAY DIFFRACTION100
3.09-3.540.21841480.15274534X-RAY DIFFRACTION99.96
3.54-4.460.15841410.144612X-RAY DIFFRACTION100
4.46-39.130.17531490.16094776X-RAY DIFFRACTION99.82
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)
13.76570871526-0.581837512336-0.3570909414654.5308312385-1.445673415996.120237559130.01731569185220.231269717414-0.496267760919-0.1650630540050.08245050456140.1731909017340.899159638574-0.0575616956118-0.08659526462340.3000275247310.0165129727329-0.01545814884350.278836329814-0.05449813480710.21016653249441.5171236361-26.7268789439-21.5190406311
23.441878408721.390399346823.488379516380.5597381172871.430879631163.913480367270.05292348312661.04242330173-0.670593611699-1.037797327830.05665178640280.7143083488080.494323608872-0.207217566734-0.207448858680.832594765745-0.0738954804062-0.2390669369720.666661438687-0.1797038311160.51923330851640.8864472348-35.7081557378-19.604910196
31.53574153523-1.300561284090.4207703813291.99880541134-1.778071007992.483601568660.03874339131570.129632766048-0.214287551265-0.0750932240354-0.01684870591860.0903616462870.0780090534951-0.171551862937-0.007805138521720.103669379696-0.00667053878974-0.01113264078960.145727235088-0.03612680661150.15126919950842.2743051018-20.4794519025-9.80049158123
41.255933230560.905069255309-0.1457714390811.37286601858-0.3903477582471.10510690553-0.03700690998480.141675741941-0.0699405105967-0.07799223166830.1196565642570.120363154640.119767522027-0.117417220534-0.09169327473990.0924027033053-0.000292987406449-0.01951734139180.142245975340.002071286283070.1158208854029.33753623817-17.4054650342-13.7418350065
51.75251532122-0.3835150851570.9667430741011.263347344940.01228950103242.444948271870.0562984491160.1176431554780.000611153355938-0.10521393506-0.00139537714083-0.04790537995270.0594332613520.130582818047-0.0639507993360.0973772186277-0.01470671729260.01546538913450.1167995994450.006005277888640.090877789330628.323291609-10.147647371-26.9848579594
62.61861173952-0.0797474649144-0.8919625449851.251803549760.09387777783342.969904990640.0883468493209-0.5200539557760.2880648139540.1940357773480.0105619807134-0.153337791334-0.1445201735990.317137553074-0.07197738011940.142132776146-0.00411522939119-0.01780465625970.184670658161-0.04120072272950.16973727595340.1956887809-17.931204647415.1851121708
74.23696489205-3.384889540131.474351217222.7441187427-1.348296551010.9731760858510.1009246085010.168982976232-0.0638497085011-0.072848780117-0.138511678892-0.0843736959210.03867205150040.07644947254780.02006486876180.111994564957-0.00982523210485-0.007333762918170.107333581858-0.01273311754260.12141316600134.3192188381-21.56466267831.93561862029
83.052872870252.016144415040.03426836947442.410243161250.2376922946220.3686876439690.009458921084120.1148882623440.309465075616-0.02668801692910.02429501196740.0268292848361-0.08078544432550.0194442659707-0.02499721155150.1376252040310.0174986238223-0.01421764442180.09979588145460.01875519186690.14573351052128.09190854579.76016366972-6.00714639436
90.718110031587-0.203620851387-0.1064559638331.07552939546-0.3867646110121.34652658471-0.0115550517035-0.0751319568760.06804755840840.1236018152020.04088901689110.0317931188367-0.140400724722-0.0561697026544-0.02888735408360.1076872685620.00210612788333-0.01104255717050.117601463535-0.005896491421180.11089100531419.5495369044-6.120919673989.47330077141
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 13 through 68 )AA13 - 681 - 56
22chain 'A' and (resid 69 through 89 )AA69 - 8957 - 77
33chain 'A' and (resid 90 through 142 )AA90 - 14278 - 130
44chain 'A' and (resid 143 through 236 )AA143 - 236131 - 222
55chain 'A' and (resid 237 through 375 )AA237 - 375223 - 346
66chain 'B' and (resid 14 through 89 )BJ14 - 891 - 76
77chain 'B' and (resid 90 through 151 )BJ90 - 15177 - 138
88chain 'B' and (resid 152 through 224 )BJ152 - 224139 - 209
99chain 'B' and (resid 225 through 373 )BJ225 - 373210 - 340

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