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- PDB-5kwv: Crystal Structure of a Pantoate-beta-alanine Ligase from Neisseri... -

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Basic information

Entry
Database: PDB / ID: 5kwv
TitleCrystal Structure of a Pantoate-beta-alanine Ligase from Neisseria gonorrhoeae with bound AMPPNP
ComponentsPantothenate synthetase
KeywordsLIGASE / SSGCID / Neisseria gonorrhoeae / pantoate-beta-alanine_ligase / AMPPNP / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


pantoate-beta-alanine ligase (AMP-forming) / pantoate-beta-alanine ligase activity / pantothenate biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Pantoate-beta-alanine ligase, C-terminal domain / Pantoate-beta-alanine ligase / Pantoate-beta-alanine ligase, C-terminal domain / Pantoate-beta-alanine ligase / Pantoate--beta-alanine Ligase; Chain: A,domain 2 / Cytidyltransferase-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 2-Layer Sandwich ...Pantoate-beta-alanine ligase, C-terminal domain / Pantoate-beta-alanine ligase / Pantoate-beta-alanine ligase, C-terminal domain / Pantoate-beta-alanine ligase / Pantoate--beta-alanine Ligase; Chain: A,domain 2 / Cytidyltransferase-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Pantothenate synthetase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of a Pantoate-beta-alanine Ligase from Neisseria gonorrhoeae with bound AMPPNP
Authors: Dranow, D.M. / Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionJul 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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_prerelease_seq / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pantothenate synthetase
B: Pantothenate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1074
Polymers64,0952
Non-polymers1,0122
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-9 kcal/mol
Surface area22970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.650, 137.650, 73.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 0:1 or (resid 2 and (name...
21(chain B and (resid 0:59 or resid 69:183 or (resid...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISMETMET(chain A and (resid 0:1 or (resid 2 and (name...AA0 - 18 - 9
12GLNGLNGLNGLN(chain A and (resid 0:1 or (resid 2 and (name...AA210
13HISHISANPANP(chain A and (resid 0:1 or (resid 2 and (name...AA - C0 - 3008
14HISHISANPANP(chain A and (resid 0:1 or (resid 2 and (name...AA - C0 - 3008
15HISHISANPANP(chain A and (resid 0:1 or (resid 2 and (name...AA - C0 - 3008
16HISHISANPANP(chain A and (resid 0:1 or (resid 2 and (name...AA - C0 - 3008
21HISHISGLYGLY(chain B and (resid 0:59 or resid 69:183 or (resid...BB0 - 598 - 67
22ARGARGSERSER(chain B and (resid 0:59 or resid 69:183 or (resid...BB69 - 18377 - 191
23ARGARGARGARG(chain B and (resid 0:59 or resid 69:183 or (resid...BB184192
24HISHISANPANP(chain B and (resid 0:59 or resid 69:183 or (resid...BB - D0 - 3008
25HISHISANPANP(chain B and (resid 0:59 or resid 69:183 or (resid...BB - D0 - 3008
26HISHISANPANP(chain B and (resid 0:59 or resid 69:183 or (resid...BB - D0 - 3008
27HISHISANPANP(chain B and (resid 0:59 or resid 69:183 or (resid...BB - D0 - 3008

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Components

#1: Protein Pantothenate synthetase / PS / Pantoate--beta-alanine ligase / Pantoate-activating enzyme


Mass: 32047.469 Da / Num. of mol.: 2 / Fragment: NegoA.00097.a.B1 / Mutation: A194G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Strain: NCCP11945 / Gene: panC, NGK_0607 / Plasmid: NegoA.00097.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B4RKE7, pantoate-beta-alanine ligase (AMP-forming)
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: NegoA.00097.a.B1.PS37929 at 20.8 mg/ml, incubated with 3 mM MgCl2, 3 mM AMPPNP, protein mixed 1:1 and incubated with an equal volume Morpheus(f12): 12.5% (w/v) PEG-1000, 12.5 % (w/v) PEG- ...Details: NegoA.00097.a.B1.PS37929 at 20.8 mg/ml, incubated with 3 mM MgCl2, 3 mM AMPPNP, protein mixed 1:1 and incubated with an equal volume Morpheus(f12): 12.5% (w/v) PEG-1000, 12.5 % (w/v) PEG-3350, 12.5% (v/v) MPD, 0.1 M bicine/Trizma base, pH = 8.5, 0.02 M each D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, N-acetyl-D-glucosamine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 22, 2016 / 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: 2.25→50 Å / Num. obs: 33816 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Biso Wilson estimate: 44.16 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.091 / Net I/σ(I): 15.33
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.25-2.310.4774.10.9321100
2.31-2.370.3765.080.9621100
2.37-2.440.2826.530.9791100
2.44-2.520.2527.410.981100
2.52-2.60.2168.640.9841100
2.6-2.690.16910.60.9911100
2.69-2.790.14812.130.9921100
2.79-2.90.1314.170.9941100
2.9-3.030.11316.420.9941100
3.03-3.180.09818.770.9951100
3.18-3.350.08921.330.996199.9
3.35-3.560.08223.050.996199.9
3.56-3.80.07924.450.9961100
3.8-4.110.07925.710.9961100
4.11-4.50.07526.20.996199.9
4.5-5.030.07326.70.9961100
5.03-5.810.07426.160.997199.9
5.81-7.120.07426.380.995199.7
7.12-10.060.07626.480.9961100
10.060.07424.490.996193.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UK2

3uk2


Resolution: 2.25→43.529 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.58
RfactorNum. reflection% reflection
Rfree0.2191 2034 6.02 %
Rwork0.183 --
obs0.1853 33807 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 159.06 Å2 / Biso mean: 57.9523 Å2 / Biso min: 25.12 Å2
Refinement stepCycle: final / Resolution: 2.25→43.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4064 0 62 157 4283
Biso mean--92.33 50.7 -
Num. residues----540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084196
X-RAY DIFFRACTIONf_angle_d0.9075726
X-RAY DIFFRACTIONf_chiral_restr0.053666
X-RAY DIFFRACTIONf_plane_restr0.006752
X-RAY DIFFRACTIONf_dihedral_angle_d18.222495
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2347X-RAY DIFFRACTION11.167TORSIONAL
12B2347X-RAY DIFFRACTION11.167TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2499-2.30230.29551320.215420682200100
2.3023-2.35990.28841210.216421112232100
2.3599-2.42370.27461390.195520692208100
2.4237-2.4950.23231290.185620892218100
2.495-2.57550.23931260.187720822208100
2.5755-2.66750.25691280.196421202248100
2.6675-2.77430.26211370.206220912228100
2.7743-2.90060.26231400.2120982238100
2.9006-3.05340.30971270.206121212248100
3.0534-3.24470.2281130.20821282241100
3.2447-3.49510.20751610.194820842245100
3.4951-3.84660.22151330.173221472280100
3.8466-4.40280.20211350.163821392274100
4.4028-5.54530.17381410.16321762317100
5.5453-43.53690.19821720.1742250242299
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)
12.8290.49970.42263.8671-0.03154.43040.1845-0.1279-0.52650.1257-0.0088-0.16670.92080.0194-0.15620.64410.07570.03520.28770.12140.430341.701169.686733.9561
22.12060.38680.6451.84070.33293.3182-0.0556-0.13110.03020.28920.0341-0.03720.02030.02440.03160.3530.02110.00630.30730.06060.311240.127586.191731.2187
32.20820.64720.2224.6296-0.54785.13830.0194-0.1074-0.20790.1695-0.1306-0.40150.05730.72210.09890.32820.0096-0.04770.60740.10370.349459.093293.232141.5634
46.13771.968-0.47863.2460.26742.8961-0.0185-0.380.21130.22310.51081.1619-0.0574-1.0704-0.16630.3716-0.04110.13860.81730.18250.80412.068986.691630.3985
52.4798-0.27590.20732.165-0.7171.9765-0.007-0.0007-0.04260.10210.26980.5250.0653-0.8258-0.04130.2592-0.0250.0540.5750.13020.41221.325989.595724.3243
66.2951-3.2864-2.03983.61780.59381.82130.01870.6082-0.2688-0.2828-0.00710.27120.0592-0.85650.00030.3450.0075-0.03570.8630.05040.374513.755594.41882.3036
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 94 )A0 - 94
2X-RAY DIFFRACTION2chain 'A' and (resid 95 through 170 )A95 - 170
3X-RAY DIFFRACTION3chain 'A' and (resid 171 through 278 )A171 - 278
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 70 )B0 - 70
5X-RAY DIFFRACTION5chain 'B' and (resid 71 through 170 )B71 - 170
6X-RAY DIFFRACTION6chain 'B' and (resid 171 through 276 )B171 - 276

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