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- PDB-2prr: Crystal structure of alkylhydroperoxidase AhpD core: uncharacteri... -

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Entry
Database: PDB / ID: 2prr
TitleCrystal structure of alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein (YP_296737.1) from Ralstonia eutropha JMP134 at 2.15 A resolution
ComponentsAlkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein
KeywordsOXIDOREDUCTASE / YP_296737.1 / Carboxymuconolactone decarboxylase family / Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


peroxiredoxin activity / peroxidase activity
Similarity search - Function
AhpD-like / Uncharacterised peroxidase-related / Alkylhydroperoxidase AhpD core / AhpD-like / AhpD-like / Carboxymuconolactone decarboxylase-like / Carboxymuconolactone decarboxylase family / AhpD-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Alkylhydroperoxidase AhpD core:Uncharacterized peroxidase-related protein
Similarity search - Component
Biological speciesRalstonia eutropha (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein (YP_296737.1) from Ralstonia eutropha JMP134 at 2.15 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 12 ... BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 12 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein
B: Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein
C: Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein
D: Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein
E: Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein
F: Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein
G: Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein
H: Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein
I: Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein
J: Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein
K: Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein
L: Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,90944
Polymers269,20512
Non-polymers3,70432
Water24,1041338
1
A: Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein
B: Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein
D: Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein
E: Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein
H: Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein
I: Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,47722
Polymers134,6026
Non-polymers1,87416
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24260 Å2
ΔGint-27 kcal/mol
Surface area40760 Å2
MethodPISA
2
C: Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein
F: Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein
G: Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein
J: Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein
K: Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein
L: Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,43322
Polymers134,6026
Non-polymers1,83016
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23650 Å2
ΔGint-39 kcal/mol
Surface area40970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.105, 93.953, 120.898
Angle α, β, γ (deg.)84.260, 81.640, 77.730
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ALA / End label comp-ID: VAL / Refine code: 5 / Auth seq-ID: 5 - 192 / Label seq-ID: 6 - 193

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH
9II
10JJ
11KK
12LL
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A HEXAMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein


Mass: 22433.742 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha (bacteria) / Species: Cupriavidus necator / Strain: JMP134 / Gene: YP_296737.1, Reut_A2532 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q46Y90
#2: Chemical...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1338 / Source method: isolated from a natural source / Formula: H2O

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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: 2.65 Å3/Da / Density % sol: 53.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.1
Details: NANODROP, 0.2M Na2HPO4, 20.0% PEG 3350, No Buffer pH 9.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97932, 0.97905
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 4, 2006 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979321
30.979051
ReflectionResolution: 1.88→48.912 Å / Num. obs: 211872 / % possible obs: 87.2 % / Biso Wilson estimate: 30.222 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 6.23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
1.88-1.950.4192357741803777.4
1.95-2.030.3782.2378311903283.1
2.03-2.120.2742.8360811815083.4
2.12-2.230.2353.2386321942287.9
2.23-2.370.1744.2383841929386.1
2.37-2.550.1375391471967488.9
2.55-2.810.1096.2400632013688.7
2.81-3.210.0768.2392881973889.1
3.210.04711.9416502093993.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.15→48.912 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.917 / SU B: 8.887 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.245 / ESU R Free: 0.208
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. POLYETHYLENE GLYCOL MOLECULES FROM THE CRYSTALLIZATION BUFFER WERE MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.262 7726 5.1 %RANDOM
Rwork0.211 ---
all0.213 ---
obs0.213 152688 94.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.806 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å2-2.42 Å2-2.97 Å2
2---0.85 Å24.05 Å2
3---0.99 Å2
Refinement stepCycle: LAST / Resolution: 2.15→48.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17690 0 245 1338 19273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02218345
X-RAY DIFFRACTIONr_bond_other_d0.0020.0217006
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.95924799
X-RAY DIFFRACTIONr_angle_other_deg0.96339224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.23252268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.1323.24855
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.693152865
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.10715145
X-RAY DIFFRACTIONr_chiral_restr0.0930.22723
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0220462
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023879
X-RAY DIFFRACTIONr_nbd_refined0.2130.34444
X-RAY DIFFRACTIONr_nbd_other0.1620.318624
X-RAY DIFFRACTIONr_nbtor_refined0.1840.59141
X-RAY DIFFRACTIONr_nbtor_other0.0890.510098
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2310.51806
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0520.59
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1090.310
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1960.364
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.512
X-RAY DIFFRACTIONr_mcbond_it1.523311738
X-RAY DIFFRACTIONr_mcbond_other0.68134555
X-RAY DIFFRACTIONr_mcangle_it2.393518288
X-RAY DIFFRACTIONr_scbond_it4.91987384
X-RAY DIFFRACTIONr_scangle_it6.123116511
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1096MEDIUM POSITIONAL0.210.5
2B1096MEDIUM POSITIONAL0.160.5
3C1096MEDIUM POSITIONAL0.220.5
4D1096MEDIUM POSITIONAL0.180.5
5E1096MEDIUM POSITIONAL0.180.5
6F1096MEDIUM POSITIONAL0.20.5
7G1096MEDIUM POSITIONAL0.20.5
8H1096MEDIUM POSITIONAL0.160.5
9I1096MEDIUM POSITIONAL0.240.5
10J1096MEDIUM POSITIONAL0.210.5
11K1096MEDIUM POSITIONAL0.190.5
12L1096MEDIUM POSITIONAL0.170.5
1A1605LOOSE POSITIONAL0.395
2B1605LOOSE POSITIONAL0.365
3C1605LOOSE POSITIONAL0.345
4D1605LOOSE POSITIONAL0.335
5E1605LOOSE POSITIONAL0.415
6F1605LOOSE POSITIONAL0.435
7G1605LOOSE POSITIONAL0.435
8H1605LOOSE POSITIONAL0.365
9I1605LOOSE POSITIONAL0.445
10J1605LOOSE POSITIONAL0.485
11K1605LOOSE POSITIONAL0.395
12L1605LOOSE POSITIONAL0.335
1A1096MEDIUM THERMAL1.532
2B1096MEDIUM THERMAL1.142
3C1096MEDIUM THERMAL1.22
4D1096MEDIUM THERMAL0.962
5E1096MEDIUM THERMAL1.082
6F1096MEDIUM THERMAL0.972
7G1096MEDIUM THERMAL1.072
8H1096MEDIUM THERMAL1.212
9I1096MEDIUM THERMAL1.022
10J1096MEDIUM THERMAL1.332
11K1096MEDIUM THERMAL1.232
12L1096MEDIUM THERMAL1.172
1A1605LOOSE THERMAL4.1410
2B1605LOOSE THERMAL3.1910
3C1605LOOSE THERMAL3.3710
4D1605LOOSE THERMAL3.110
5E1605LOOSE THERMAL3.2610
6F1605LOOSE THERMAL2.8610
7G1605LOOSE THERMAL3.5110
8H1605LOOSE THERMAL3.0510
9I1605LOOSE THERMAL3.2310
10J1605LOOSE THERMAL3.3310
11K1605LOOSE THERMAL3.6310
12L1605LOOSE THERMAL3.4710
LS refinement shellHighest resolution: 2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 570 -
Rwork0.369 10812 -
obs-11382 95.61 %

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