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- PDB-4f3r: Structure of phosphopantetheine adenylyltransferase (CBU_0288) fr... -

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Basic information

Entry
Database: PDB / ID: 4f3r
TitleStructure of phosphopantetheine adenylyltransferase (CBU_0288) from Coxiella burnetii
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / phosphopantetheine adenylyltranferase
Function / homology
Function and homology information


pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Phosphopantetheine adenylyltransferase / Cytidylyltransferase-like / Cytidyltransferase-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsFranklin, M.C. / Cheung, J. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionMay 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Oct 21, 2015Group: Database references
Revision 1.3Feb 10, 2016Group: Database references
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
C: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2484
Polymers55,2083
Non-polymers401
Water3,333185
1
A: Phosphopantetheine adenylyltransferase

A: Phosphopantetheine adenylyltransferase

A: Phosphopantetheine adenylyltransferase


Theoretical massNumber of molelcules
Total (without water)55,2083
Polymers55,2083
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area3260 Å2
ΔGint-32 kcal/mol
Surface area21810 Å2
MethodPISA
2
B: Phosphopantetheine adenylyltransferase
hetero molecules

B: Phosphopantetheine adenylyltransferase
hetero molecules

B: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3296
Polymers55,2083
Non-polymers1203
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area3390 Å2
ΔGint-55 kcal/mol
Surface area23090 Å2
MethodPISA
3
C: Phosphopantetheine adenylyltransferase

C: Phosphopantetheine adenylyltransferase

C: Phosphopantetheine adenylyltransferase


Theoretical massNumber of molelcules
Total (without water)55,2083
Polymers55,2083
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area3110 Å2
ΔGint-29 kcal/mol
Surface area23020 Å2
MethodPISA
4
A: Phosphopantetheine adenylyltransferase

A: Phosphopantetheine adenylyltransferase

A: Phosphopantetheine adenylyltransferase

C: Phosphopantetheine adenylyltransferase

C: Phosphopantetheine adenylyltransferase

C: Phosphopantetheine adenylyltransferase


Theoretical massNumber of molelcules
Total (without water)110,4176
Polymers110,4176
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_665x-y+1,-y+1,-z1
crystal symmetry operation6_655-x+1,-x+y,-z1
Buried area14150 Å2
ΔGint-132 kcal/mol
Surface area37040 Å2
MethodPISA
5
B: Phosphopantetheine adenylyltransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)110,65712
Polymers110,4176
Non-polymers2406
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area15130 Å2
ΔGint-176 kcal/mol
Surface area37830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.965, 103.965, 89.862
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Phosphopantetheine adenylyltransferase / Dephospho-CoA pyrophosphorylase / Pantetheine-phosphate adenylyltransferase / PPAT / CBU_0288 protein


Mass: 18402.770 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA 493 Nine Mile Phase I / Gene: CBU_0288, coaD / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q83EM7, pantetheine-phosphate adenylyltransferase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Tri-sodium citrate, 20% w/v PEG 3000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 23, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.25→100 Å / Num. all: 27264 / Num. obs: 27253 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 21.5 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 43.6
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 21.4 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 4.2 / Num. unique all: 1347 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.25→45.02 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.923 / SU B: 12.906 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.275 / ESU R Free: 0.204
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23643 1367 5 %RANDOM
Rwork0.20995 ---
obs0.2113 25882 99.94 %-
all-27265 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.256 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20.39 Å20 Å2
2--0.79 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 2.25→45.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3485 0 1 185 3671
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223575
X-RAY DIFFRACTIONr_bond_other_d0.0010.022399
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.9874877
X-RAY DIFFRACTIONr_angle_other_deg0.79935874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4715442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.47323.613155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.43815588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2271524
X-RAY DIFFRACTIONr_chiral_restr0.0640.2579
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213906
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02706
X-RAY DIFFRACTIONr_mcbond_it0.5641.52222
X-RAY DIFFRACTIONr_mcbond_other0.0931.5875
X-RAY DIFFRACTIONr_mcangle_it1.11523632
X-RAY DIFFRACTIONr_scbond_it1.8531353
X-RAY DIFFRACTIONr_scangle_it3.2134.51242
LS refinement shellResolution: 2.25→2.302 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 101 -
Rwork0.254 1861 -
obs--99.34 %
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)
13.1397-1.2669-0.8513.38680.73674.43510.1014-0.17120.1510.20090.1641-0.0052-0.16960.0883-0.26550.0839-0.04330.01290.20040.04490.116333.168124.334915.0776
24.1559-1.22380.37083.2101-1.11943.40610.10390.3229-0.0211-0.26570.06760.15170.2669-0.1329-0.17150.1266-0.02970.01020.04540.00680.02226.08418.813332.0618
35.92490.3999-1.08542.5847-0.78223.43680.0172-0.33560.19110.15760.14210.1886-0.2155-0.1653-0.15930.1970.002-0.03520.11790.0650.0745-4.644140.790210.4067
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 153
2X-RAY DIFFRACTION2B1 - 154
3X-RAY DIFFRACTION3C1 - 154

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