[English] 日本語
Yorodumi
- PDB-3l5o: Crystal structure of protein with unknown function from DUF364 fa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3l5o
TitleCrystal structure of protein with unknown function from DUF364 family (ZP_00559375.1) from Desulfitobacterium hafniense DCB-2 at 2.01 A resolution
Componentsuncharacterized protein from DUF364 family
KeywordsAdenosyl binding protein / rare metals / siderophores / adenosyl binding site / protein with unknown function from DUF364 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Enolase-like; domain 1 - #100 / Rossmann fold - #11590 / Putative heavy-metal chelation domain / Domain of unknown function DUF4213 / Putative heavy-metal chelation / Putative heavy-metal chelation / Enolase-like; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / Uncharacterized protein
Similarity search - Component
Biological speciesDesulfitobacterium hafniense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å
AuthorsJoint Center for Structural Genomics / Joint Center for Structural Genomics (JCSG)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structure of the first representative of Pfam family PF04016 (DUF364) reveals enolase and Rossmann-like folds that combine to form a unique active site with a possible role in heavy-metal chelation.
Authors: Miller, M.D. / Aravind, L. / Bakolitsa, C. / Rife, C.L. / Carlton, D. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Chiu, H.J. / Clayton, T. / Deller, M.C. / Duan, L. / Feuerhelm, J. / ...Authors: Miller, M.D. / Aravind, L. / Bakolitsa, C. / Rife, C.L. / Carlton, D. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Chiu, H.J. / Clayton, T. / Deller, M.C. / Duan, L. / Feuerhelm, J. / Grant, J.C. / Han, G.W. / Jaroszewski, L. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Kozbial, P. / Krishna, S.S. / Kumar, A. / Marciano, D. / McMullan, D. / Morse, A.T. / Nigoghossian, E. / Okach, L. / Reyes, R. / van den Bedem, H. / Weekes, D. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionDec 22, 2009Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 2, 2010ID: 2H1Q
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: uncharacterized protein from DUF364 family
B: uncharacterized protein from DUF364 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,64514
Polymers60,9252
Non-polymers72012
Water4,288238
1
A: uncharacterized protein from DUF364 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7606
Polymers30,4631
Non-polymers2985
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: uncharacterized protein from DUF364 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8858
Polymers30,4631
Non-polymers4227
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-12 kcal/mol
Surface area20170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.640, 120.640, 75.200
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1 - 127
2116B1 - 127
1126A143 - 251
2126B143 - 251

NCS ensembles :
ID
1
2

-
Components

#1: Protein uncharacterized protein from DUF364 family


Mass: 30462.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfitobacterium hafniense (bacteria)
Strain: DCB-2 / DSM 10664 / Gene: Dhaf_4260 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: B8FUJ5
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1.0M LiCl, 0.1M citrate pH 5.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97915
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 29, 2006 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.01→28.977 Å / Num. obs: 41624 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.48 % / Biso Wilson estimate: 35.519 Å2 / Rmerge F obs: 0.12 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.066 / Net I/σ(I): 12.26 / Num. measured all: 311344
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.01-2.080.8530.6681.821252798378320.81598.1
2.08-2.170.6320.5162.425108875087410.62699.9
2.17-2.260.4430.3733.321380747374630.45399.9
2.26-2.380.3340.2844.323798825282440.34499.9
2.38-2.530.2180.191623796824682350.23199.9
2.53-2.730.1550.135824119834483340.16399.9
2.73-30.1030.11411.931851804280360.13199.9
3-3.430.0530.07919.645056814181350.08899.9
3.43-4.320.0280.04928.647824820081960.054100
4.320.020.03936.347160826181920.04299.2

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.01→28.977 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.761 / SU ML: 0.109 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.14
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. 3. CHLORIDE (CL), IMIDAZOL (IMD), AND ETHYLENE GLYCOL (EDO) HAVE BEEN MODELED ADDED BASED ON CRYSTALLIZATION CONDITIONS, PROTEIN BUFFER AND CRYOPROTECTANT. 4. RESIDUES A103-109 AND B103-114 ARE DISORDERED AND WERE NOT MODELED. 5. RESIDUE B117 (GLU) IS A RAMACHANDRAN OUTLIER, AND IS LOCATED IN WEAK DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.215 2092 5 %RANDOM
Rwork0.171 39491 --
obs0.173 41583 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 115.76 Å2 / Biso mean: 52.382 Å2 / Biso min: 28.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20.18 Å20 Å2
2--0.35 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 2.01→28.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3695 0 46 238 3979
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213842
X-RAY DIFFRACTIONr_bond_other_d0.0020.023536
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9735222
X-RAY DIFFRACTIONr_angle_other_deg0.84638180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3655497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52823.933150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18315592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1671521
X-RAY DIFFRACTIONr_chiral_restr0.0890.2594
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024297
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02762
X-RAY DIFFRACTIONr_nbd_refined0.2010.2750
X-RAY DIFFRACTIONr_nbd_other0.2250.24061
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21849
X-RAY DIFFRACTIONr_nbtor_other0.0840.22228
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2180
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1210.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2820.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.212
X-RAY DIFFRACTIONr_mcbond_it2.00732523
X-RAY DIFFRACTIONr_mcbond_other0.48931000
X-RAY DIFFRACTIONr_mcangle_it3.03753954
X-RAY DIFFRACTIONr_scbond_it4.77481496
X-RAY DIFFRACTIONr_scangle_it6.505111263
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
11608LOOSE POSITIONAL0.435
11608LOOSE THERMAL2.5110
21604LOOSE POSITIONAL0.465
21604LOOSE THERMAL2.1110
LS refinement shellResolution: 2.009→2.061 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 178 -
Rwork0.225 2874 -
all-3052 -
obs--99.97 %
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)
14.2782-0.850.41651.31320.42631.0282-0.027-0.4760.23060.183-0.0034-0.05720.0626-0.24880.0304-0.2757-0.0308-0.0097-0.08140.0216-0.07472.06147.44266.212
23.0540.1773-1.21170.8941-0.44272.44990.02930.3752-0.0181-0.2249-0.03860.0780.1236-0.40570.0092-0.22040.0707-0.011-0.1958-0.0171-0.105717.74942.18935.329
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 251
2X-RAY DIFFRACTION2B-4 - 251

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more