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- PDB-2vec: The crystal structure of the protein YhaK from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 2vec
TitleThe crystal structure of the protein YhaK from Escherichia coli
ComponentsPIRIN-LIKE PROTEIN YHAK
KeywordsCYTOSOLIC PROTEIN / ROS / BICUPIN / SULFENIC ACID / REACTIVE CYSTEINE
Function / homology
Function and homology information


Quercetin 2,3-dioxygenase, C-terminal cupin domain / Quercetinase C-terminal cupin domain / Pirin, N-terminal domain / Pirin / Pirin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Pirin-like protein YhaK
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGurmu, D. / Lu, J. / Johnson, K.A. / Nordlund, P. / Holmgren, A. / Erlandsen, H.
CitationJournal: Proteins / Year: 2008
Title: The Crystal Structure of the Protein Yhak from Escherichia Coli Reveals a New Subclass of Redox Sensitive Enterobacterial Bicupins.
Authors: Gurmu, D. / Lu, J. / Johnson, K.A. / Nordlund, P. / Holmgren, A. / Erlandsen, H.
History
DepositionOct 18, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 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
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_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PIRIN-LIKE PROTEIN YHAK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6893
Polymers28,6181
Non-polymers712
Water2,036113
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)57.648, 57.648, 162.092
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PIRIN-LIKE PROTEIN YHAK / YHAK


Mass: 28618.371 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-233
Source method: isolated from a genetically manipulated source
Details: CYS122 IS OXIDIZED TO A SULFENIC ACID. AN INTRAMOLECULAR DISULFIDE BOND BETWEEN CYS10 AND CYS204.
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42624
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 5 / Details: 0.1 M CITRIC ACID, PH 5.0, 2.0 M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9797
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 25, 2005 / Details: MIRROR
RadiationMonochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.85→36.42 Å / Num. obs: 23745 / % possible obs: 97.8 % / Observed criterion σ(I): 4 / Redundancy: 19.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 28
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 19.3 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 4.3 / % possible all: 92.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→21.75 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.13 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1214 5.1 %RANDOM
Rwork0.182 ---
obs0.183 22438 97.6 %-
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: 34.74 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å20 Å2
2--1.52 Å20 Å2
3----3.04 Å2
Refinement stepCycle: LAST / Resolution: 1.85→21.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1779 0 2 113 1894
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211831
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.671.9572488
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.2835.087230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.46324.2789
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69815299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.721511
X-RAY DIFFRACTIONr_chiral_restr0.1350.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021420
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.2721
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21211
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2130
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0781.51176
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.46321808
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4873755
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9344.5679
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: 1.85→1.9 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.239 85
Rwork0.214 1490
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)
11.0088-0.45140.10674.0289-0.05473.99780.04910.05460.2261-0.3299-0.024-0.4991-0.41040.4355-0.0251-0.0145-0.05720.0322-0.09220.0026-0.027-3.9521.13267.131
21.0582-0.40630.15932.5426-0.54723.3694-0.0006-0.0916-0.0234-0.08240.15710.3527-0.1772-0.5352-0.1565-0.08050.0123-0.0386-0.05180.0414-0.0396-20.073-2.70874.136
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 134
2X-RAY DIFFRACTION2A135 - 233

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