[English] 日本語
Yorodumi
- PDB-1b7p: VERIFICATION OF SPMP USING MUTANT HUMAN LYSOZYMES -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1b7p
TitleVERIFICATION OF SPMP USING MUTANT HUMAN LYSOZYMES
ComponentsPROTEIN (LYSOZYME)
KeywordsHYDROLASE / MUTANT STABILITY / HUMAN LYSOZYME
Function / homology
Function and homology information


antimicrobial humoral response / azurophil granule lumen / specific granule lumen / retina homeostasis / tertiary granule lumen / lysozyme / lysozyme activity / killing of cells of other organism / cytolysis / defense response to Gram-negative bacterium ...antimicrobial humoral response / azurophil granule lumen / specific granule lumen / retina homeostasis / tertiary granule lumen / lysozyme / lysozyme activity / killing of cells of other organism / cytolysis / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / inflammatory response / defense response to bacterium / cellular protein metabolic process / neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding
C-type lysozyme/alpha-lactalbumin family / Lysozyme C / Lysozyme-like domain superfamily / Glycoside hydrolase, family 22, conserved site / Glycoside hydrolase, family 22 / Glycoside hydrolase, family 22, lysozyme / Lysozyme - #10 / Lysozyme / Orthogonal Bundle / Mainly Alpha
Lysozyme C
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2 Å
AuthorsTakano, K. / Ota, M. / Ogasahara, K. / Yamagata, Y. / Nishikawa, K. / Yutani, K.
Citation
Journal: Protein Eng. / Year: 1999
Title: Experimental verification of the 'stability profile of mutant protein' (SPMP) data using mutant human lysozymes.
Authors: Takano, K. / Ota, M. / Ogasahara, K. / Yamagata, Y. / Nishikawa, K. / Yutani, K.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: A General Rule for the Relationship between Hydrophobic Effect and Conformational Stability of a Protein: Stability and Structure of a Series of Hydrophobic Mutants of Human Lysozyme
Authors: Takano, K. / Yamagata, Y. / Yutani, K.
#2: Journal: Biochemistry / Year: 1998
Title: Contribution of Hydrogen Bonds to the Conformational Stability of Human Lysozyme: Calorimetry and X-Ray Analysis of Six Tyrosine->Phenylalanine Mutants
Authors: Yamagata, Y. / Kubota, M. / Sumikawa, Y. / Funahashi, J. / Takano, K. / Fujii, S. / Yutani, K.
#3: Journal: Biochemistry / Year: 1997
Title: Contribution of the Hydrophobic Effect to the Stability of Human Lysozyme: Calorimetric Studies and X-Ray Structural Analyses of the Nine Valine to Alanine Mutants
Authors: Takano, K. / Yamagata, Y. / Fujii, S. / Yutani, K.
#4: Journal: J.Mol.Biol. / Year: 1997
Title: Contribution of Water Molecules in the Interior of a Protein to the Conformational Stability
Authors: Takano, K. / Funahashi, J. / Yamagata, Y. / Fujii, S. / Yutani, K.
#5: Journal: J.Mol.Biol. / Year: 1995
Title: Contribution of Hydrophobic Residues to the Stability of Human Lysozyme: Calorimetric Studies and X-Ray Structural Analysis of the Five Isoleucine to Valine Mutants
Authors: Takano, K. / Ogasawaha, K. / Kaneda, H. / Yamagata, Y. / Fujii, S. / Kanaya, E. / Kikuchi, M. / Oobatake, M. / Yutani, K.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMay 8, 1998Processing site: RCSB
Revision 1.0Jan 25, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (LYSOZYME)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6632
Polymers14,6401
Non-polymers231
Water4,107228
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)56.300, 61.490, 33.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein/peptide PROTEIN (LYSOZYME)


Mass: 14639.598 Da / Num. of mol.: 1 / Mutation: H78G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P61626, lysozyme
#2: Chemical ChemComp-NA / SODIUM ION / Sodium


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 1.98 Å3/Da / Density % sol: 38.03 %
Crystal growpH: 4.5 / Details: pH 4.5
Crystal grow
*PLUS
Temperature: 10 ℃ / Method: vapor diffusion, hanging drop / Details: Takano, K., (1995) J.Mol.Biol., 254, 62.
Components of the solutions
*PLUS

Crystal-ID: 1

IDConc.Common nameSol-IDChemical formula
110 mg/mlproteindrop
22.5 MreservoirNaCl
320 mMacetatereservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 4, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 43893 / % possible obs: 60.4 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.062
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.155 / Mean I/σ(I) obs: 3.3 / % possible all: 46.2
Reflection
*PLUS
Num. obs: 6618 / Num. measured all: 43893

-
Processing

Software
NameVersionClassification
PROCESSdata collection
PROCESSdata reduction
X-PLORmodel building
X-PLOR3.1refinement
PROCESSdata scaling
X-PLORphasing
RefinementMethod to determine structure: OTHER
Starting model: WILD-TYPE OF HUMAN LYSOZYME

Resolution: 2→8 Å / σ(F): 3
RfactorNum. reflection% reflection
Rwork0.146 --
Obs-4929 62.1 %
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1023 0 1 228 1252
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2→2.09 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.188 502 -
Obs--54.1 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / σ(F): 3 / Rfactor obs: 0.146
LS refinement shell
*PLUS
Highest resolution: 2 Å / Rfactor Rwork: 0.188

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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