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- PDB-2ejc: Crystal Structure Of Pantoate--Beta-Alanine Ligase (panC) From Th... -

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Basic information

Entry
Database: PDB / ID: 2ejc
TitleCrystal Structure Of Pantoate--Beta-Alanine Ligase (panC) From Thermotoga maritima
ComponentsPantoate--beta-alanine ligase
KeywordsLIGASE / Pantoate-beta-alanine ligase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


pantoate-beta-alanine ligase (AMP-forming) / pantoate-beta-alanine ligase activity / pantothenate biosynthetic process / ATP binding / cytosol
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
ACETATE ION / Pantothenate synthetase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBagautdinov, B. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure Of Pantoate--Beta-Alanine Ligase (panC) From Thermotoga maritima
Authors: Bagautdinov, B. / Kunishima, N.
History
DepositionMar 16, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pantoate--beta-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,30624
Polymers32,8081
Non-polymers1,49823
Water3,585199
1
A: Pantoate--beta-alanine ligase
hetero molecules

A: Pantoate--beta-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,61248
Polymers65,6152
Non-polymers2,99646
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area7320 Å2
ΔGint-1309.6 kcal/mol
Surface area25880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.182, 85.182, 90.372
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-1138-

HOH

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Components

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


Mass: 32807.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: panC / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): (DE3)RIL
References: UniProt: Q9X0G6, pantoate-beta-alanine ligase (AMP-forming)
#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.88 Å3/Da / Density % sol: 57.35 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 6.5
Details: 9w/v(%) PEG 8000, 0.1M Cacodylate, 0.2M zinc acetate, pH 6.5, microbatch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 22, 2006 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→38.53 Å / Num. all: 15251 / Num. obs: 15225 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 43.5 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.053 / Net I/σ(I): 11.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1506 / Rsym value: 0.406 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V8F

1v8f


Resolution: 2.4→38.53 Å / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.286 767 -RANDOM
Rwork0.211 ---
obs0.211 15225 99.8 %-
all-15251 --
Displacement parametersBiso mean: 37.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å22.55 Å20 Å2
2--0.66 Å20 Å2
3----1.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.4→38.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2300 0 26 199 2525
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0.037
RfactorNum. reflection% reflection
Rfree0.338 85 -
Rwork0.248 --
obs-1508 99.8 %

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