[English] 日本語
Yorodumi
- PDB-4m6d: Crystal structure of the aptamer minF-lysozyme complex. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4m6d
TitleCrystal structure of the aptamer minF-lysozyme complex.
Components
  • Lysozyme C
  • aptamer
KeywordsHydrolase/RNA / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium / Hydrolase-RNA complex
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily ...Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA / RNA (> 10) / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.68 Å
AuthorsMalashkevich, V.N. / Padlan, F.C. / Toro, R. / Girvin, M. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of the aptamer minF-lysozyme complex.
Authors: Malashkevich, V.N. / Padlan, F.C. / Toro, R. / Girvin, M. / Almo, S.C.
History
DepositionAug 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Advisory / Database references / Structure summary
Category: audit_author / citation_author / pdbx_unobs_or_zero_occ_atoms
Item: _audit_author.name / _citation_author.name
Revision 1.2Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lysozyme C
B: aptamer
C: Lysozyme C
D: aptamer
E: Lysozyme C
F: aptamer
G: Lysozyme C
H: aptamer
I: Lysozyme C
J: aptamer
K: Lysozyme C
L: aptamer


Theoretical massNumber of molelcules
Total (without water)173,11712
Polymers173,11712
Non-polymers00
Water1,24369
1
A: Lysozyme C
B: aptamer


Theoretical massNumber of molelcules
Total (without water)28,8532
Polymers28,8532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Lysozyme C
D: aptamer


Theoretical massNumber of molelcules
Total (without water)28,8532
Polymers28,8532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Lysozyme C
F: aptamer


Theoretical massNumber of molelcules
Total (without water)28,8532
Polymers28,8532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Lysozyme C
H: aptamer


Theoretical massNumber of molelcules
Total (without water)28,8532
Polymers28,8532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Lysozyme C
J: aptamer


Theoretical massNumber of molelcules
Total (without water)28,8532
Polymers28,8532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Lysozyme C
L: aptamer


Theoretical massNumber of molelcules
Total (without water)28,8532
Polymers28,8532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.914, 132.289, 131.539
Angle α, β, γ (deg.)118.59, 96.39, 96.27
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14331.160 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ, lyz1 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: P00698, lysozyme
#2: RNA chain
aptamer


Mass: 14521.679 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: minF
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.78 Å3/Da / Density % sol: 67.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.1M Malonic Acid, 0.15 M Ammonium Citrate Tribasic, 0.072 M Succinic Acid, 0.18 M DL-Malic Acid, 0.24 M Sodium Acetate, 0.3 M Sodium Formate, 0.096 M Ammonium Tartrate Dibasic, Final pH 7. ...Details: 1.1M Malonic Acid, 0.15 M Ammonium Citrate Tribasic, 0.072 M Succinic Acid, 0.18 M DL-Malic Acid, 0.24 M Sodium Acetate, 0.3 M Sodium Formate, 0.096 M Ammonium Tartrate Dibasic, Final pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 18, 2013
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.351
11-H, H+K+L, -L20.014
11-H, -L, -K30.015
11H, L, -H-K-L40.344
11H, -H-K-L, K50.267
11-H, -K, H+K+L60.009
ReflectionResolution: 2.68→50 Å / Num. obs: 67209 / % possible obs: 94.9 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.7-2.751.80.629190.9
2.75-2.81.80.571191.5
2.8-2.851.80.491192.6
2.85-2.911.80.38192.1
2.91-2.971.80.358193.3
2.97-3.041.80.278195.7
3.04-3.121.80.234194.6
3.12-3.21.90.189195.6
3.2-3.31.90.153197.1
3.3-3.41.90.127195.1
3.4-3.521.90.117198.3
3.52-3.661.90.103195.7
3.66-3.831.90.088197.6
3.83-4.031.90.07195.5
4.03-4.291.90.061196.7
4.29-4.621.90.055195.6
4.62-5.081.90.051196.7
5.08-5.811.90.047196.8
5.81-7.321.90.042195.6
7.32-501.90.037190.6

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.41 Å37.82 Å
Translation6.41 Å37.82 Å

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.5.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4M4O

4m4o


Resolution: 2.68→38.04 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.915 / Occupancy max: 1 / Occupancy min: 0 / SU B: 20.942 / SU ML: 0.198 / SU R Cruickshank DPI: 0.1634 / Cross valid method: THROUGHOUT / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. ORIGINALLY DATA WERE PROCESSED IN H3, WITH ONE RNA:PROTEIN HETERDIMER PER ASYMMETRIC UNIT. BUT REFINEMENT STATISTICS WERE AROUND 0.32/0.36. ...Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. ORIGINALLY DATA WERE PROCESSED IN H3, WITH ONE RNA:PROTEIN HETERDIMER PER ASYMMETRIC UNIT. BUT REFINEMENT STATISTICS WERE AROUND 0.32/0.36. THE REFINEMENT STATISTICS ARE MUCH BETTER WHEN DATA PROCESSED IN P1, INDICATING DIFFERENCES BETWEEN SUBUNITS.
RfactorNum. reflection% reflectionSelection details
Rfree0.216 3007 5.3 %RANDOM
Rwork0.16549 ---
obs0.16832 53394 79.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 122.84 Å2
Baniso -1Baniso -2Baniso -3
1--33.08 Å2-1.5 Å2-4.37 Å2
2--74.15 Å2-12.52 Å2
3----41.07 Å2
Refinement stepCycle: LAST / Resolution: 2.68→38.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6006 5357 0 69 11432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01512133
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.57217653
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.515768
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.80923.131297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.93615996
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6771563
X-RAY DIFFRACTIONr_chiral_restr0.0940.21864
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027368
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.26311.3573090
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.8783852
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.99515.2129043
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr8.222312133
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded53.84511360
LS refinement shellResolution: 2.685→2.754 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 13 -
Rwork0.196 338 -
obs--6.64 %
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)
11.17790.77230.32132.36960.74970.29320.0506-0.0258-0.135-0.0105-0.0091-0.37710.07660.042-0.04150.22790.07050.03420.4258-0.09970.3336-2.969-37.59-29.807
22.11680.18040.33673.837-0.63882.9442-0.52410.68050.6364-0.2013-0.31890.4377-0.08430.15620.8430.5224-0.008-0.18930.947-0.0850.5589-25.676-48.064-56.111
31.6210.62320.5333.78140.71820.6339-0.067-0.10640.22430.0710.03590.3319-0.1358-0.12350.0310.21030.04330.05620.4162-0.12980.3367-22.025-17.267-18.462
46.29883.0799-2.94723.2331-1.18941.443-0.0655-0.3072-0.2807-0.5221-0.1539-0.3671-0.10250.1430.21940.47450.0718-0.18160.7015-0.11780.61611.00710.776-22.45
51.6284-0.66890.62922.4575-1.23440.927-0.03410.18710.12690.0654-0.1638-0.4533-0.1410.17650.19790.26660.00050.01010.46080.04750.3603-2.78744.493-19.824
61.064-0.5989-0.5573.12150.03370.3951-0.1903-0.00330.16140.56870.14730.47930.029-0.08440.0430.54050.0621-0.10880.6044-0.13690.6229-25.51272.576-15.698
71.1365-1.25010.9032.589-1.65211.65560.1530.0185-0.2627-0.02440.08340.3959-0.013-0.0706-0.23640.2431-0.0097-0.0280.47740.06380.3609-21.96824.425-8
81.4395-0.10441.34611.4847-0.61441.5729-0.15060.04210.41810.0507-0.1739-0.3506-0.10110.14910.32440.64420.08240.01750.52210.05930.47031.01213.98818.214
91.41340.0611-0.53460.09960.33591.5490.039-0.0827-0.05940.03030.0374-0.03020.06390.1-0.07640.28020.0192-0.02080.465-0.01240.0183-2.816-4.69346.028
102.991-0.1716-1.24721.0589-0.60631.2196-0.3525-0.0974-0.4556-0.28540.30110.30610.46620.05110.05140.47220.07490.00490.6140.09860.154-25.558-22.18968.174
111.4143-0.0733-1.1640.44190.44592.89250.1430.14340.0249-0.08240.0288-0.0131-0.111-0.181-0.17180.2110.0244-0.02110.4442-0.07520.0384-21.962-4.99922.831
124.215-2.258-1.53081.60921.18110.93770.027-0.4057-0.4670.0967-0.0091-0.00620.2419-0.0383-0.01790.5085-0.02790.06780.7067-0.0780.40491.319-23.0090.489
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999
5X-RAY DIFFRACTION5E-10 - 9999
6X-RAY DIFFRACTION6F-10 - 9999
7X-RAY DIFFRACTION7G-10 - 9999
8X-RAY DIFFRACTION8H-10 - 9999
9X-RAY DIFFRACTION9I-10 - 9999
10X-RAY DIFFRACTION10J-10 - 9999
11X-RAY DIFFRACTION11K-10 - 9999
12X-RAY DIFFRACTION12L-10 - 9999

+
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