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

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Basic information

Entry
Database: PDB / ID: 5ucr
TitleCrystal Structure of a Pantoate-beta-alanine Ligase from Neisseria gonorrhoeae with bound AMPPNP and Alanine
ComponentsPantothenate synthetase
KeywordsLIGASE / SSGCID / 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
ALANINE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Pantothenate synthetase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 2.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle 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 and Alanine
Authors: Dranow, D.M. / Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionDec 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,1378
Polymers63,8332
Non-polymers1,3046
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-21 kcal/mol
Surface area22300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.650, 137.650, 72.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 31916.273 Da / Num. of mol.: 2 / 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: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H7NO2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.71 Å3/Da / Density % sol: 54.56 %
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(h12): 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(h12): 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 sodium L-glutamate, DL-alanine, DL-lysine, DL-serine

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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: Nov 9, 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→40.485 Å / Num. obs: 33764 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 9.634 % / Biso Wilson estimate: 46.57 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Net I/σ(I): 23.99
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2% possible all
2.25-2.319.9230.4943.91244690.937100
2.31-2.379.9080.3925.030.958100
2.37-2.449.9290.2986.530.976100
2.44-2.529.9180.2687.520.979100
2.52-2.69.9070.229.270.983100
2.6-2.699.8920.15912.450.992100
2.69-2.799.8480.14214.440.993100
2.79-2.99.8760.11118.020.996100
2.9-3.039.8140.09322.070.997100
3.03-3.189.7130.07527.120.998100
3.18-3.359.5970.0633.460.99899.9
3.35-3.569.4820.05138.170.99999.9
3.56-3.89.3180.04542.610.99999.9
3.8-4.119.210.04146.540.99999.9
4.11-4.59.1830.03749.660.99999.6
4.5-5.039.0940.03451.770.99999.6
5.03-5.819.1760.03350.350.99999.5
5.81-7.129.1540.0351.990.99999.5
7.12-10.068.7720.02654.260.99999.6
10.06-40.4857.4270.02550.160.99994.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_2621refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5KWV

5kwv


Resolution: 2.25→40.485 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22
RfactorNum. reflection% reflection
Rfree0.2171 1689 5 %
Rwork0.1735 --
obs0.1756 33750 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 132.21 Å2 / Biso mean: 57.3488 Å2 / Biso min: 28.64 Å2
Refinement stepCycle: final / Resolution: 2.25→40.485 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4045 0 93 168 4306
Biso mean--71.31 52.72 -
Num. residues----537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074211
X-RAY DIFFRACTIONf_angle_d0.8835743
X-RAY DIFFRACTIONf_chiral_restr0.052673
X-RAY DIFFRACTIONf_plane_restr0.005752
X-RAY DIFFRACTIONf_dihedral_angle_d18.6182509
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.31620.24761380.218526222760100
2.3162-2.3910.2531390.20326332772100
2.391-2.47640.24951380.194226312769100
2.4764-2.57550.26491380.192326182756100
2.5755-2.69270.22771400.190426582798100
2.6927-2.83470.26531390.200926432782100
2.8347-3.01220.27571400.203126552795100
3.0122-3.24470.23841410.20526762817100
3.2447-3.5710.2191390.181126632802100
3.571-4.08740.19181430.161126992842100
4.0874-5.1480.18011430.139827192862100
5.148-40.49110.20671510.16462844299599
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)
14.2461-0.13541.62844.0463-0.16574.58550.1786-0.1066-0.43190.2252-0.0817-0.18840.65940.1618-0.0980.58670.080.06020.28870.12840.436441.772970.135433.8469
22.78690.55180.53982.38680.59523.1754-0.0931-0.05960.08210.16880.0114-0.0115-0.06660.11510.0940.36830.02750.03940.3450.09010.326939.848586.153731.1464
32.0320.52540.45375.0618-0.4174.37530.0329-0.1132-0.07420.148-0.1016-0.43640.01010.45860.08490.3109-0.0159-0.02440.52960.10490.290358.799693.185541.3445
41.99982.00023.422522.00025.2313-1.5753-0.92272.8698-1.12940.3902-4.6111-0.39310.98861.25571.17410.34820.15130.66630.00171.124145.964780.169331.1217
57.64561.36580.11292.81180.04133.4798-0.1646-0.30880.06180.29570.35850.87240.0151-0.8561-0.17940.37340.00580.19430.7220.14940.706711.589785.911630.2625
63.0332-0.27070.47092.7058-0.86962.6726-0.06310.02220.05250.12320.19380.4731-0.0511-0.6174-0.02640.24440.01840.0820.47650.09660.431720.982189.609924.1583
76.8212-3.3421-2.10714.22350.13182.31480.01110.6693-0.0842-0.35310.00610.17280.0644-0.7494-0.01190.3304-0.0064-0.05260.75640.04750.358513.618394.69682.3194
88.7943-1.497-2.61557.29111.225320.6471-1.0316-2.8468-2.4910.14968.2719-0.8914-5.23-0.86250.7270.63870.1590.97810.57132.380217.170892.335323.5742
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 'A' and (resid 301 through 301 )A301
5X-RAY DIFFRACTION5chain 'B' and (resid 0 through 70 )B0 - 70
6X-RAY DIFFRACTION6chain 'B' and (resid 71 through 170 )B71 - 170
7X-RAY DIFFRACTION7chain 'B' and (resid 171 through 275 )B171 - 275
8X-RAY DIFFRACTION8chain 'B' and (resid 301 through 301 )B301

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