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- PDB-2g6g: Crystal structure of MltA from Neisseria gonorrhoeae -

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Basic information

Entry
Database: PDB / ID: 2g6g
TitleCrystal structure of MltA from Neisseria gonorrhoeae
ComponentsGNA33
KeywordsHYDROLASE / BETA BARREL
Function / homology
Function and homology information


: / peptidoglycan turnover / outer membrane / hydrolase activity, hydrolyzing O-glycosyl compounds / cell wall organization / lyase activity
Similarity search - Function
MltA, 3D domain / Barwin-like endoglucanases / Lytic transglycosylase MltA, domain B / Membrane-bound lytic murein transglycosylase A / MltA specific insert domain / MltA specific insert domain / 3D domain / 3D domain / RlpA-like domain / RlpA-like domain superfamily ...MltA, 3D domain / Barwin-like endoglucanases / Lytic transglycosylase MltA, domain B / Membrane-bound lytic murein transglycosylase A / MltA specific insert domain / MltA specific insert domain / 3D domain / 3D domain / RlpA-like domain / RlpA-like domain superfamily / Ribosomal Protein L25; Chain P / Barwin-like endoglucanases / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesNeisseria gonorrhoeae FA 1090 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsPowell, A.J. / Liu, Z.J. / Nicholas, R.A. / Davies, C.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structures of the Lytic Transglycosylase MltA from N.gonorrhoeae and E.coli: Insights into Interdomain Movements and Substrate Binding.
Authors: Powell, A.J. / Liu, Z.J. / Nicholas, R.A. / Davies, C.
History
DepositionFeb 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GNA33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1009
Polymers46,3391
Non-polymers7618
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.06, 87.26, 111.95
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GNA33 / MLTA


Mass: 46339.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae FA 1090 (bacteria)
Species: Neisseria gonorrhoeae / Strain: ATCC 700825 / FA 1090 / Gene: GNA33 / Plasmid: pMAL-c2KV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21*
References: UniProt: Q5F581, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.53 Å3/Da / Density % sol: 51.41 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG 8000, 0.2 M ammonium sulphate, 100 mM sodium cacodylate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97934, 0.97967, 0.97492
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 26, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979341
20.979671
30.974921
ReflectionResolution: 2.2→44 Å / Num. all: 24576 / Num. obs: 24576 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 38.6
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 5.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→44 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.909 / SU B: 12.538 / SU ML: 0.16 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25932 1253 5.1 %RANDOM
Rwork0.21254 ---
obs0.21487 24548 99.91 %-
all-24548 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.166 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å20 Å2
2---1.27 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.2→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3128 0 42 94 3264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223251
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9654406
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3015403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.34222.603146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.99615501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4111528
X-RAY DIFFRACTIONr_chiral_restr0.0970.2451
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022518
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.21309
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22131
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2166
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7151.52043
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.15823198
X-RAY DIFFRACTIONr_scbond_it1.80431370
X-RAY DIFFRACTIONr_scangle_it2.7214.51208
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 85 -
Rwork0.282 1668 -
obs--99.55 %
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)
11.96440.4553-0.76442.74840.84791.78650.08450.07730.12560.13050.1625-0.22190.19330.0886-0.247-0.35280.013-0.0611-0.0517-0.0422-0.20375.41548.22253.615
22.2715-1.22060.68613.276-2.01699.17890.1442-0.19070.0210.08530.28150.03511.4311-0.7114-0.4257-0.0538-0.1583-0.0504-0.10790.0245-0.3073-4.26623.60534.679
35.2003-0.47073.15084.1911-2.08867.46060.0159-0.17830.20760.29390.21640.236-0.348-0.6131-0.2323-0.31510.01930.0705-0.03280.0618-0.2072-8.7440.97717.458
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 51
2X-RAY DIFFRACTION1A52 - 64
3X-RAY DIFFRACTION1A65 - 76
4X-RAY DIFFRACTION1A77 - 92
5X-RAY DIFFRACTION1A93 - 97
6X-RAY DIFFRACTION1A98 - 107
7X-RAY DIFFRACTION1A108 - 112
8X-RAY DIFFRACTION1A113 - 121
9X-RAY DIFFRACTION1A122 - 130
10X-RAY DIFFRACTION1A131 - 142
11X-RAY DIFFRACTION1A343 - 349
12X-RAY DIFFRACTION1A350 - 355
13X-RAY DIFFRACTION1A356 - 362
14X-RAY DIFFRACTION1A363 - 369
15X-RAY DIFFRACTION1A370 - 380
16X-RAY DIFFRACTION1A381 - 392
17X-RAY DIFFRACTION1A393 - 402
18X-RAY DIFFRACTION1A403 - 411
19X-RAY DIFFRACTION1A412 - 421
20X-RAY DIFFRACTION1A422 - 433
21X-RAY DIFFRACTION1A434 - 441
22X-RAY DIFFRACTION2A143 - 149
23X-RAY DIFFRACTION2A150 - 162
24X-RAY DIFFRACTION2A163 - 166
25X-RAY DIFFRACTION2A230 - 239
26X-RAY DIFFRACTION2A240 - 243
27X-RAY DIFFRACTION2A244 - 253
28X-RAY DIFFRACTION2A254 - 263
29X-RAY DIFFRACTION2A264 - 271
30X-RAY DIFFRACTION2A272 - 283
31X-RAY DIFFRACTION2A284 - 289
32X-RAY DIFFRACTION2A290 - 297
33X-RAY DIFFRACTION2A306 - 313
34X-RAY DIFFRACTION2A314 - 320
35X-RAY DIFFRACTION2A321 - 328
36X-RAY DIFFRACTION2A329 - 337
37X-RAY DIFFRACTION3A167 - 173
38X-RAY DIFFRACTION3A174 - 176
39X-RAY DIFFRACTION3A177 - 189
40X-RAY DIFFRACTION3A190 - 194
41X-RAY DIFFRACTION3A195 - 200
42X-RAY DIFFRACTION3A201 - 206
43X-RAY DIFFRACTION3A207 - 213
44X-RAY DIFFRACTION3A214 - 223
45X-RAY DIFFRACTION3A224 - 229

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