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- PDB-2jdj: crystal structure of HapK from Hahella chejuensis -

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Basic information

Entry
Database: PDB / ID: 2jdj
Titlecrystal structure of HapK from Hahella chejuensis
ComponentsREDY-LIKE PROTEIN
KeywordsBIOSYNTHETIC PROTEIN / PRODIGIOSIN / BIOSYNTHESIS
Function / homologyREDY-like protein HapK / REDY-like protein HapK / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / ISOPROPYL ALCOHOL / RedY-like protein
Function and homology information
Biological speciesHAHELLA CHEJUENSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsKang, B.S. / Cho, H.J. / Kim, K.J.
CitationJournal: Proteins / Year: 2008
Title: Structural Insight of the Role of the Hahella Chejuensis Hapk Protein in Prodigiosin Biosynthesis.
Authors: Cho, H.J. / Kim, K. / Kim, M.H. / Kang, B.S.
History
DepositionJan 10, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 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 / pdbx_struct_special_symmetry / struct_conn
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_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: REDY-LIKE PROTEIN
B: REDY-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,40012
Polymers23,5912
Non-polymers80910
Water3,009167
1
A: REDY-LIKE PROTEIN
hetero molecules

A: REDY-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,40012
Polymers23,5912
Non-polymers80910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556-y,-x,-z+4/31
Buried area3510 Å2
ΔGint-16.4 kcal/mol
Surface area11850 Å2
MethodPQS
2
B: REDY-LIKE PROTEIN
hetero molecules

B: REDY-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,40012
Polymers23,5912
Non-polymers80910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_666-y+1,-x+1,-z+4/31
Buried area3470 Å2
ΔGint-17.3 kcal/mol
Surface area11860 Å2
MethodPQS
Unit cell
Length a, b, c (Å)58.306, 58.306, 137.882
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11B-17-

ASP

21A-2006-

HOH

31A-2022-

HOH

41B-2009-

HOH

51B-2025-

HOH

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Components

#1: Protein REDY-LIKE PROTEIN / HAPK


Mass: 11795.713 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HAHELLA CHEJUENSIS (bacteria) / Strain: KCTC2396 / Plasmid: PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q2S9J0
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsABB69083.1

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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: 2.7 Å3/Da / Density % sol: 53.4 % / Description: NONE
Crystal growpH: 6.5 / Details: 1.8 M AMMONIUM SULFATE, 7% ISOPROPANOL, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.97949
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 5, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 35383 / % possible obs: 100 % / Observed criterion σ(I): 8 / Redundancy: 11 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 44
Reflection shellResolution: 2→2.07 Å / Redundancy: 11 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 8.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2→28.52 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.098 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 918 5.2 %RANDOM
Rwork0.189 ---
obs0.191 16842 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2→28.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1640 0 48 167 1855
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221720
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3051.9472334
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7735210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.34324.25387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6415255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1961510
X-RAY DIFFRACTIONr_chiral_restr0.0860.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021316
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.2725
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21186
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2154
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.289
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8311.51075
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.20321678
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9073725
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9264.5655
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→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.232 69
Rwork0.232 1202

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