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- PDB-4mv2: Crystal structure of plu4264 protein from Photorhabdus luminescens -

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Basic information

Entry
Database: PDB / ID: 4mv2
TitleCrystal structure of plu4264 protein from Photorhabdus luminescens
Componentsplu4264
KeywordsUNKNOWN FUNCTION / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Enzyme Discovery for Natural Product Biosynthesis / NatPro / cupin
Function / homology
Function and homology information


Polyketide biosynthesis protein CurC, predicted / : / Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17
Similarity search - Component
Biological speciesPhotorhabdus luminescens subsp. laumondii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.349 Å
AuthorsMichalska, K. / Li, H. / Jedrzejczak, R. / Babnigg, G. / Bingman, C.A. / Yennamalli, R. / Weerth, S. / Thomas, M.G. / Phillips Jr., G.N. / Joachimiak, A. ...Michalska, K. / Li, H. / Jedrzejczak, R. / Babnigg, G. / Bingman, C.A. / Yennamalli, R. / Weerth, S. / Thomas, M.G. / Phillips Jr., G.N. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
CitationJournal: Proteins / Year: 2015
Title: Structure of a cupin protein Plu4264 from Photorhabdus luminescens subsp. laumondii TTO1 at 1.35 angstrom resolution.
Authors: Weerth, R.S. / Michalska, K. / Bingman, C.A. / Yennamalli, R.M. / Li, H. / Jedrzejczak, R. / Wang, F. / Babnigg, G. / Joachimiak, A. / Thomas, M.G. / Phillips, G.N.
History
DepositionSep 23, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionOct 2, 2013ID: 4I4A
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Source and taxonomy
Revision 1.2Nov 12, 2014Group: Database references
Revision 1.3Feb 4, 2015Group: Database references
Revision 1.4Oct 30, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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: plu4264
B: plu4264
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2765
Polymers31,1362
Non-polymers1403
Water5,206289
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-66 kcal/mol
Surface area11720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.738, 147.687, 83.843
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein plu4264


Mass: 15567.780 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus luminescens subsp. laumondii (bacteria)
Strain: TT01 / Gene: plu4264 / Plasmid: pMCSG81 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: Q7MZL9
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.77 Å3/Da / Density % sol: 55.61 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Li2SO4, 0.1 M Tris/HCl 8.5, 25% PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2012 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. all: 76260 / Num. obs: 76134 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 26.8
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.891 / Mean I/σ(I) obs: 2 / Num. unique all: 3769 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXmodel building
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
Cootmodel building
PHENIX(phenix.refine: dev_1446)refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.349→24.898 Å / SU ML: 0.12 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 15.92 / Stereochemistry target values: ML / Details: hydrogen atoms have been added at riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1589 1113 1.46 %random
Rwork0.1355 ---
all0.1359 76091 --
obs0.1359 76091 99.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.349→24.898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2028 0 3 289 2320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132429
X-RAY DIFFRACTIONf_angle_d1.4613335
X-RAY DIFFRACTIONf_dihedral_angle_d13.313893
X-RAY DIFFRACTIONf_chiral_restr0.095349
X-RAY DIFFRACTIONf_plane_restr0.007444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3493-1.41070.23691250.20179240X-RAY DIFFRACTION99
1.4107-1.4850.18961550.15169274X-RAY DIFFRACTION100
1.485-1.5780.17281360.12279330X-RAY DIFFRACTION100
1.578-1.69990.11921230.1039330X-RAY DIFFRACTION100
1.6999-1.87090.14431440.10039347X-RAY DIFFRACTION100
1.8709-2.14150.14811270.1099423X-RAY DIFFRACTION100
2.1415-2.69750.14481540.13539417X-RAY DIFFRACTION100
2.6975-24.90190.16851490.15449617X-RAY DIFFRACTION99

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