[English] 日本語
Yorodumi
- PDB-3ksv: Hypothetical protein from Leishmania major -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ksv
TitleHypothetical protein from Leishmania major
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / HIT family / Structural Genomics / Structural Genomics of Pathogenic Protozoa Consortium / SGPP
Function / homology
Function and homology information


nucleotide metabolic process / catalytic activity / metal ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2230 / HINT family / Histidine triad (HIT) protein / HIT domain / Histidine triad, conserved site / HIT domain signature. / HIT domain profile. / HIT-like domain / HIT-like / HIT family, subunit A ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2230 / HINT family / Histidine triad (HIT) protein / HIT domain / Histidine triad, conserved site / HIT domain signature. / HIT domain profile. / HIT-like domain / HIT-like / HIT family, subunit A / HIT-like superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
HIT domain-containing protein
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsHan, G.W. / Merritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: To be Published
Title: Hypothetical protein (HIT family) from Leishmania major
Authors: Merritt, E.A. / Le Trong, I. / Han, G.W. / Kalyuzhniy, O. / Mehlin, C. / Van Voorhis, W.C. / Buckner, F.S. / Fan, E. / Zucker, F. / Verlinde, L.M.J. / Hol, W.G.J.
History
DepositionNov 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 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.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3072
Polymers16,2421
Non-polymers651
Water43224
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6144
Polymers32,4832
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area6680 Å2
ΔGint-51 kcal/mol
Surface area12340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.628, 67.764, 76.182
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Uncharacterized protein


Mass: 16241.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: uncleaved / Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LmjF14.0240 / Plasmid: PET14B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 STAR / References: UniProt: Q4QFW1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.09 Å3/Da / Density % sol: 41.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9.2
Details: protein buffer 25 mM HEPES pH 7.25, 125 mM NaCl; crystallization buffer 0.1 M TRIX/Glycine pH 9.2, 0.2 M MgCl2, 28% PEG 4000, vapor diffusion, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9784 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 8, 2003
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9784 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 8847 / % possible obs: 79.5 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.067 / Χ2: 1.097 / Net I/σ(I): 13.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.975.80.2295860.949153.8
1.97-2.0560.1896310.929157.1
2.05-2.146.20.1586831.055162.7
2.14-2.256.30.137421.267167.4
2.25-2.396.40.1098331.237176.4
2.39-2.586.60.1078991.179182.5
2.58-2.846.60.0910771.03195.6
2.84-3.2570.08311031.105199.7
3.25-4.096.80.06111291.048199.9
4.09-406.60.04711641.106197.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.5.0096refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.24 / WRfactor Rwork: 0.206 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.158 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.045 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.226 414 4.7 %RANDOM
Rwork0.198 ---
obs0.2 8787 79.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 74.71 Å2 / Biso mean: 23.938 Å2 / Biso min: 9.66 Å2
Baniso -1Baniso -2Baniso -3
1--44.61 Å20 Å20 Å2
2--102.01 Å20 Å2
3----57.4 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1049 0 1 24 1074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221068
X-RAY DIFFRACTIONr_bond_other_d0.0010.02696
X-RAY DIFFRACTIONr_angle_refined_deg1.3111.9551447
X-RAY DIFFRACTIONr_angle_other_deg0.87731722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1315140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.31225.47642
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02415181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.983153
X-RAY DIFFRACTIONr_chiral_restr0.0780.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211194
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02188
X-RAY DIFFRACTIONr_mcbond_it0.5981.5701
X-RAY DIFFRACTIONr_mcbond_other0.1261.5284
X-RAY DIFFRACTIONr_mcangle_it1.15521120
X-RAY DIFFRACTIONr_scbond_it1.8693367
X-RAY DIFFRACTIONr_scangle_it3.0644.5327
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.9490.362200.27240982152.253
1.949-2.0020.17170.26641376356.356
2.002-2.060.302130.23543377057.922
2.06-2.1230.289260.21344674663.271
2.123-2.1920.261230.20945071965.786
2.192-2.2690.287240.18844369367.388
2.269-2.3540.253310.21247465776.865
2.354-2.450.215230.18748965378.407
2.45-2.5590.319280.21849262882.803
2.559-2.6830.211200.20854261491.531
2.683-2.8280.26350.21452256498.759
2.828-2.9980.215250.23650353099.623
2.998-3.2040.163210.23148750999.804
3.204-3.4590.247170.209462479100
3.459-3.7870.257260.1842244999.777
3.787-4.2290.206220.17238040599.259
4.229-4.8750.154210.1534036499.176
4.875-5.950.209100.17629330699.02
5.95-8.330.31280.1924025198.805
8.33-41.5620.12540.20813315687.821
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)
110.30530.5068-9.844231.62122.7767.88970.06850.655-0.5844-0.9355-0.21752.3730.9314-1.32550.1490.4573-0.2557-0.16740.67240.09370.4599-20.586-15.9152-14.7426
22.39360.1542-0.76840.57310.10633.34940.0896-0.06140.20950.04730.00810.1692-0.2913-0.4781-0.09770.20180.03130.02660.26290.00080.2389-9.0964-11.2446-11.7623
33.39020.12660.77611.44810.54484.65080.0418-0.2001-0.19730.055-0.0037-0.01390.3132-0.0029-0.0380.2035-0.01120.02420.18070.02810.2391-0.9519-19.6741-12.9916
41.65390.5581-1.65420.67170.58095.3184-0.0010.2191-0.1287-0.2124-0.00080.07580.3810.01070.00180.24240.0133-0.01560.295-0.04730.29712.8094-19.9307-33.1398
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 7
2X-RAY DIFFRACTION2A8 - 68
3X-RAY DIFFRACTION3A69 - 109
4X-RAY DIFFRACTION4A110 - 141

+
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://pdbjlc1.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