[English] 日本語
Yorodumi
- PDB-3lb5: Crystal structure of Hit-like protein involved in cell-cycle regu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3lb5
TitleCrystal structure of Hit-like protein involved in cell-cycle regulation from Bartonella henselae with unknown ligand
ComponentsHit-like protein involved in cell-cycle regulation
KeywordsCELL CYCLE / NIAID / Seattle Structural Genomics Center for Infectious Disease / SSGCID / histidine triad / HIT / histidine triad nucleotide binding protein / HINT / unknown ligand / bacteremia / cat-scratch disease / Bartonellosis
Function / homology
Function and homology information


HINT family / Histidine triad (HIT) protein / HIT domain / HIT domain profile. / HIT-like domain / HIT-like / HIT family, subunit A / HIT-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / Hit-like protein involved in cell-cycle regulation / Hit-like protein involved in cell-cycle regulation
Similarity search - Component
Biological speciesBartonella henselae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of Hit-like protein involved in cell-cycle regulation from Bartonella henselae with unknown ligand
Authors: Edwards, T.E. / Abendroth, J. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionJan 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hit-like protein involved in cell-cycle regulation
B: Hit-like protein involved in cell-cycle regulation
C: Hit-like protein involved in cell-cycle regulation
D: Hit-like protein involved in cell-cycle regulation


Theoretical massNumber of molelcules
Total (without water)72,4118
Polymers72,4114
Non-polymers04
Water6,395355
1
A: Hit-like protein involved in cell-cycle regulation
B: Hit-like protein involved in cell-cycle regulation


Theoretical massNumber of molelcules
Total (without water)36,2064
Polymers36,2062
Non-polymers02
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-17 kcal/mol
Surface area11790 Å2
MethodPISA
2
C: Hit-like protein involved in cell-cycle regulation
D: Hit-like protein involved in cell-cycle regulation


Theoretical massNumber of molelcules
Total (without water)36,2064
Polymers36,2062
Non-polymers02
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-18 kcal/mol
Surface area12070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.710, 97.920, 111.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A3 - 140
2116B3 - 140
3116C3 - 140
4116D3 - 140

-
Components

#1: Protein
Hit-like protein involved in cell-cycle regulation


Mass: 18102.795 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella henselae (bacteria) / Gene: BH06190 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6G5D3, UniProt: A0A0H3M325*PLUS
#2: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 4 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE COORDINATES OF LIGAND UNL RESEMBLES NICOTINAMIDE. BUT NICOTINAMIDE WAS NOT ADDED TO THE SAMPLE. ...THE COORDINATES OF LIGAND UNL RESEMBLES NICOTINAMIDE. BUT NICOTINAMIDE WAS NOT ADDED TO THE SAMPLE. IT CAN BE PART OF SOME OTHER NUCLEOBASE OF A PYRIMIDINE.

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PACT screen condition B8, 0.2 M ammonium chloride, 0.1 M MES pH 6.0, 20% PEG 6000, 25% EG as cryo-protectant; crystal tracking ID 202910b8; tag not removed prior to crystallization, VAPOR ...Details: PACT screen condition B8, 0.2 M ammonium chloride, 0.1 M MES pH 6.0, 20% PEG 6000, 25% EG as cryo-protectant; crystal tracking ID 202910b8; tag not removed prior to crystallization, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 75981 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 26.426 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 17.36
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 2.3 / Num. measured obs: 15334 / Num. unique all: 5338 / Num. unique obs: 5338 / % possible all: 94.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 57.16 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å32.57 Å
Translation3 Å32.57 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3imi

3imi


Resolution: 1.9→19.47 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.166 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.868 / SU B: 7.654 / SU ML: 0.103 / SU R Cruickshank DPI: 0.17 / SU Rfree: 0.159 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1982 5 %RANDOM
Rwork0.182 ---
obs0.184 39631 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 42.97 Å2 / Biso mean: 12.896 Å2 / Biso min: 2.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20 Å2
2---0.35 Å20 Å2
3---0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4122 0 36 355 4513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224258
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.9695780
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0225532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.34125184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.2615737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2091520
X-RAY DIFFRACTIONr_chiral_restr0.0920.2680
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213192
X-RAY DIFFRACTIONr_mcbond_it0.6091.52674
X-RAY DIFFRACTIONr_mcangle_it1.0724341
X-RAY DIFFRACTIONr_scbond_it1.92631584
X-RAY DIFFRACTIONr_scangle_it3.064.51434
Refine LS restraints NCS

Ens-ID: 1 / Number: 971 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.385
2BLOOSE POSITIONAL0.385
3CLOOSE POSITIONAL0.495
4DLOOSE POSITIONAL0.395
1ALOOSE THERMAL1.4110
2BLOOSE THERMAL1.6310
3CLOOSE THERMAL2.1410
4DLOOSE THERMAL1.6310
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 140 -
Rwork0.222 2602 -
all-2742 -
obs--94.94 %
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)
11.50360.02040.15432.0745-0.19040.9990.0626-0.03520.10820.0174-0.0540.0094-0.1752-0.041-0.00870.0783-0.03030.00310.0523-0.00730.014419.62627.3841-24.3884
21.00170.0314-0.21581.8133-0.25661.3245-0.0174-0.0069-0.0073-0.139-0.0526-0.15830.10460.17740.070.0441-0.01430.01330.05630.01390.016825.7236-14.6338-24.9186
32.8517-0.308-0.67361.52270.28230.994-0.06770.05990.00930.02110.05990.0884-0.0273-0.17110.00780.0554-0.01080.00360.0678-0.00670.0104-11.8422-18.4113-1.5688
41.65420.0634-0.26251.81360.13040.6493-0.063-0.0977-0.15220.0767-0.01180.0230.08910.05040.07470.0492-0.01370.01550.02310.00890.01946.3871-31.4138-6.5209
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 140
2X-RAY DIFFRACTION1A141
3X-RAY DIFFRACTION1A177 - 271
4X-RAY DIFFRACTION2B3 - 140
5X-RAY DIFFRACTION2B141
6X-RAY DIFFRACTION2B272 - 354
7X-RAY DIFFRACTION3C3 - 140
8X-RAY DIFFRACTION3C141
9X-RAY DIFFRACTION3C355 - 429
10X-RAY DIFFRACTION4D4 - 140
11X-RAY DIFFRACTION4D141
12X-RAY DIFFRACTION4D430 - 531

+
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