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- PDB-2x3f: Crystal Structure of the Methicillin-Resistant Staphylococcus aur... -

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Basic information

Entry
Database: PDB / ID: 2x3f
TitleCrystal Structure of the Methicillin-Resistant Staphylococcus aureus Sar2676, a Pantothenate Synthetase.
ComponentsPANTHOTHENATE SYNTHETASE
KeywordsLIGASE / ATP-BINDING / NUCLEOTIDE-BINDING / PANTOTHENATE BIOSYNTHESIS
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 / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / Pantothenate synthetase
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS SUBSP. AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsOke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / White, M.F. / Naismith, J.H.
Citation
Journal: J.Struct.Funct.Genom. / Year: 2010
Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs.
Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / Falconer, H. / Powers, H. / Overton, I.M. / Van Niekerk, C.A.J. / Peng, X. / Patel, P. / Garrett, R.A. / Prangishvili, D. / Botting, C.H. / Coote, P.J. / Dryden, D.T.F. / Barton, G.J. / Schwarz-Linek, U. / Challis, G.L. / Taylor, G.L. / White, M.F. / Naismith, J.H.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Purification, Crystallization and Data Collection of Methicillin-Resistant Staphylococcus Aureus Sar2676, a Pantothenate Synthetase.
Authors: Seetharamappa, J. / Oke, M. / Liu, H. / Mcmahon, S.A. / Johnson, K.A. / Carter, L. / Dorward, M. / Zawadzki, M. / Overton, I.M. / Van Niekirk, C.A.J. / Graham, S. / Botting, C.H. / Taylor, G. ...Authors: Seetharamappa, J. / Oke, M. / Liu, H. / Mcmahon, S.A. / Johnson, K.A. / Carter, L. / Dorward, M. / Zawadzki, M. / Overton, I.M. / Van Niekirk, C.A.J. / Graham, S. / Botting, C.H. / Taylor, G.L. / White, M.F. / Barton, G.J. / Coote, P.J. / Naismith, J.H.
History
DepositionJan 24, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: PANTHOTHENATE SYNTHETASE
B: PANTHOTHENATE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2755
Polymers63,1682
Non-polymers1,1063
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-28.81 kcal/mol
Surface area24510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.194, 86.560, 141.573
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 PANTHOTHENATE SYNTHETASE / PANTOATE--BETA-ALANINE LIGASE / PANTOATE-ACTIVATING ENZYME / PS


Mass: 31584.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS SUBSP. AUREUS (bacteria)
Strain: MRSA252 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q6GDK5, pantoate-beta-alanine ligase (AMP-forming)
#2: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 6.5
Details: 10% PEG 8000, 0.1M NA MES PH6.5, 0.2M ZN ACETATE WITH 11.5MGML-1 AMP-CPP. THE CRYSTALS WERE CRYOPROTECTED WITH OIL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 11, 2007 / Details: TOROIDAL ZERODUR MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.95→28.59 Å / Num. obs: 39073 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.5
Reflection shellResolution: 1.95→2 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.5.0090refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V8F

1v8f


Resolution: 1.95→28.59 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.926 / SU B: 8.227 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS THE STRUCTURE IS ONLY ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS THE STRUCTURE IS ONLY ORDERED FROM RESIDUE 2 TO 282
RfactorNum. reflection% reflectionSelection details
Rfree0.23752 2066 5 %RANDOM
Rwork0.20023 ---
obs0.2021 39073 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.115 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2--0.05 Å2-0 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.95→28.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4390 0 67 222 4679
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224572
X-RAY DIFFRACTIONr_bond_other_d0.0010.023024
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.9826213
X-RAY DIFFRACTIONr_angle_other_deg0.82537444
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7155571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.87824.925201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27815813
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0981522
X-RAY DIFFRACTIONr_chiral_restr0.0690.2724
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024997
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02857
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5141.52807
X-RAY DIFFRACTIONr_mcbond_other0.1271.51146
X-RAY DIFFRACTIONr_mcangle_it0.94324568
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.68631765
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8644.51639
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.951→2.002 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 152 -
Rwork0.207 2770 -
obs--98.32 %
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)
12.1677-0.38860.08122.04720.04091.9796-0.0773-0.02890.22830.02910.0125-0.0533-0.17650.04960.06470.0202-0.0062-0.01660.00580.00320.031540.54552.30647.837
22.40280.62470.24640.69580.42421.2209-0.10630.0244-0.1066-0.11810.0593-0.20920.10180.1890.0470.05510.01310.06580.03640.01320.102845.72344.10148.529
30.47890.3315-0.59890.49690.10222.7369-0.08330.0857-0.0372-0.10460.0317-0.04090.0724-0.07090.05160.0287-0.00750.00590.02950.00420.016735.14241.56939.945
47.1047-3.5322-6.75211.83653.97211.18220.25790.1686-0.0249-0.1113-0.0583-0.0225-0.1418-0.0078-0.19970.1273-0.0409-0.01270.14010.00770.138439.5645.11736.469
53.10960.6365-0.08691.89180.40692.83760.00980.2016-0.1697-0.212-0.04410.04540.1009-0.08110.03440.0968-0.0146-0.00190.0285-0.00980.04732.84433.26523.912
61.97080.5016-0.04392.20540.07191.5235-0.0303-0.01870.25110.06920.06090.0242-0.1865-0.1131-0.03070.03030.0219-0.00310.0178-0.00230.042617.15950.31966.586
72.7966-1.4309-0.91882.1040.17170.8889-0.1610.0812-0.13050.20620.09740.26860.2257-0.27150.06360.1172-0.0560.03080.1282-0.02150.067812.41243.00863.932
80.544-0.2365-0.82630.451-0.51913.6823-0.0712-0.031-0.11310.05330.02440.10710.1154-0.07450.04690.0463-0.01590.00430.0474-0.01070.061222.78337.98272.243
98.73890.4897-5.26393.46490.87263.5683-0.1015-0.14070.01320.15510.09540.06680.11550.1240.00620.08970.0151-0.0070.0862-0.0040.077918.09840.62676.095
102.4344-0.674-1.18573.26750.36472.6112-0.0064-0.0544-0.1549-0.0019-0.09260.1060.11860.06850.09910.06050.0061-0.02140.0202-0.01010.039126.08226.43885.64
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 66
2X-RAY DIFFRACTION2A67 - 111
3X-RAY DIFFRACTION3A112 - 196
4X-RAY DIFFRACTION4A1283
5X-RAY DIFFRACTION5A197 - 282
6X-RAY DIFFRACTION6B1 - 66
7X-RAY DIFFRACTION7B67 - 111
8X-RAY DIFFRACTION8B112 - 196
9X-RAY DIFFRACTION9B1283
10X-RAY DIFFRACTION10B197 - 282

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