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- PDB-4bg2: X-ray Crystal Structure of PatF from Prochloron didemni -

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Basic information

Entry
Database: PDB / ID: 4bg2
TitleX-ray Crystal Structure of PatF from Prochloron didemni
ComponentsPATF
KeywordsTRANSFERASE / PATELLAMIDE / CYANOBACTINS / NATURAL PRODUCTS / PRENYL TRANSFERASES
Function / homologyPeptide O-prenyltransferase, LynF/TruF/PatF family / Family of unknown function (DUF5838) / PatF
Function and homology information
Biological speciesPROCHLORON DIDEMNI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.13 Å
AuthorsBent, A.F. / Koehnke, J. / Houssen, W.E. / Smith, M.C.M. / Jaspars, M. / Naismith, J.H.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Structure of Patf from Prochloron Didemni.
Authors: Bent, A.F. / Koehnke, J. / Houssen, W.E. / Smith, M.C.M. / Jaspars, M. / Naismith, J.H.
History
DepositionMar 22, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Nov 6, 2013Group: Structure summary
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_sheet
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 / _pdbx_entry_details.has_protein_modification / _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_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PATF
B: PATF


Theoretical massNumber of molelcules
Total (without water)74,3812
Polymers74,3812
Non-polymers00
Water1,54986
1
A: PATF


Theoretical massNumber of molelcules
Total (without water)37,1901
Polymers37,1901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PATF


Theoretical massNumber of molelcules
Total (without water)37,1901
Polymers37,1901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.080, 135.800, 48.738
Angle α, β, γ (deg.)90.00, 118.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PATF


Mass: 37190.438 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PROCHLORON DIDEMNI (bacteria) / Plasmid: PJEXPRESS411 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q52QJ2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsNO N-TERMINAL METHIONINE AND ADDITIONAL TWO AMINO ACIDS AT C-TERMINUS (RS) DUE TO CLONING.

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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: 1.85 Å3/Da / Density % sol: 33.53 % / Description: NONE
Crystal growpH: 7.4
Details: 0.1 M SODIUM-POTASSIUM TARTRATE, 26 % PEG 2K MME, pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.13→35.32 Å / Num. obs: 29355 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 9.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14
Reflection shellResolution: 2.13→2.19 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 3.5 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
PHENIXAUTOSOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.13→35.32 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 11.011 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.326 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES A2, A197-A204, A308-A322, B197-B204, B308-B322 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.22092 1489 5.1 %RANDOM
Rwork0.18996 ---
obs0.19157 27836 97.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.791 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å2-0.25 Å2
2---1.9 Å20 Å2
3---0.9 Å2
Refinement stepCycle: LAST / Resolution: 2.13→35.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4838 0 0 86 4924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194970
X-RAY DIFFRACTIONr_bond_other_d0.0030.024665
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.9566709
X-RAY DIFFRACTIONr_angle_other_deg0.9323.00110722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg65599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61123.797266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40715869
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9951542
X-RAY DIFFRACTIONr_chiral_restr0.0770.2725
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025662
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021224
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.13→2.185 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 108 -
Rwork0.228 2023 -
obs--97.44 %
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)
14.0284-11.6321-3.200937.767511.33834.13170.06870.0254-0.215-0.1504-0.15290.494-0.05780.17030.08430.0998-0.0491-0.02590.1386-0.00510.214123.20318.914-5.352
23.32780.20380.42061.92230.09992.036-0.03350.1471-0.103-0.1394-0.0076-0.1498-0.07030.02240.04110.01810.00720.01570.05460.0020.022332.92836.9292.394
31.4889-0.40670.09211.53970.41493.1177-0.0155-0.2256-0.10150.2661-0.05730.09460.0592-0.29220.07280.0665-0.01010.0270.09830.01660.02325.37340.3417.668
47.6027-16.8884.601241.461-10.74633.5332-0.19060.11880.47610.13370.2455-0.3039-0.35550.1557-0.05490.1824-0.13380.08630.18550.04560.349748.29188.225.555
53.59750.1024-0.22152.54930.68162.5073-0.0940.08890.1227-0.13970.07580.1730.15150.02950.01820.0323-0.003-0.00350.04550.01790.030338.03271.97812.904
62.4467-0.0957-0.10471.5934-0.29432.7170.034-0.44080.09070.38690.0194-0.12240.15250.3162-0.05330.16620.03310.00750.1531-0.02570.051245.24668.9228.286
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 17
2X-RAY DIFFRACTION2A18 - 157
3X-RAY DIFFRACTION3A158 - 306
4X-RAY DIFFRACTION4B1 - 21
5X-RAY DIFFRACTION5B22 - 153
6X-RAY DIFFRACTION6B154 - 306

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