[English] 日本語
Yorodumi
- PDB-1qae: THE ACTIVE SITE OF SERRATIA ENDONUCLEASE CONTAINS A CONSERVED MAG... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qae
TitleTHE ACTIVE SITE OF SERRATIA ENDONUCLEASE CONTAINS A CONSERVED MAGNESIUM-WATER CLUSTER
ComponentsPROTEIN (EXTRACELLULAR ENDONUCLEASE)
KeywordsENDONUCLEASE / NUCLEASE / DNASE / RNASE / SUGAR-NONSPECIFIC NUCLEASE / MAGNESIUM
Function / homology
Function and homology information


Serratia marcescens nuclease / single-stranded DNA endodeoxyribonuclease activity / RNA endonuclease activity / nucleic acid binding / extracellular region / metal ion binding
Similarity search - Function
DNA/RNA non-specific endonuclease, active site / DNA/RNA non-specific endonucleases active site. / Non-specific endonuclease / Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / Extracellular Endonuclease, subunit A / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease ...DNA/RNA non-specific endonuclease, active site / DNA/RNA non-specific endonucleases active site. / Non-specific endonuclease / Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / Extracellular Endonuclease, subunit A / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease superfamily / His-Me finger superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.05 Å
AuthorsMiller, M.D. / Krause, K.L.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: The active site of Serratia endonuclease contains a conserved magnesium-water cluster.
Authors: Miller, M.D. / Cai, J. / Krause, K.L.
#1: Journal: Protein Sci. / Year: 1996
Title: Identification of the Serratia Endonuclease Dimer: Structural Basis and Implications for Catalysis
Authors: Miller, M.D. / Krause, K.L.
#2: Journal: Nat.Struct.Biol. / Year: 1994
Title: 2.1 Angstroms Structure of Serratia Endonuclease Suggests a Mechanism for Binding to Double-Stranded DNA
Authors: Miller, M.D. / Tanner, J. / Alpaugh, M. / Benedik, M.J. / Krause, K.L.
History
DepositionMar 3, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.5Apr 3, 2024Group: Data collection / Database references ...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_struct_conn_angle / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: PROTEIN (EXTRACELLULAR ENDONUCLEASE)
B: PROTEIN (EXTRACELLULAR ENDONUCLEASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5264
Polymers53,4782
Non-polymers492
Water4,522251
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.700, 74.500, 68.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (-0.999819, -0.018722, -0.003478), (-0.018758, 0.999769, 0.010535), (0.00328, 0.010599, -0.999938)
Vector: -1.0876, -0.5639, 103.2304)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 5 .. A 245 B 5 .. B 245 0.131

-
Components

#1: Protein PROTEIN (EXTRACELLULAR ENDONUCLEASE)


Mass: 26738.896 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Strain: SM6 / Cellular location: EXTRACELLULAR
Plasmid details: PLASMID WHICH ENCODES THE GENE AND CARRIES AN OPERATOR CONSTITUTIVE MUTATION
Plasmid: PUC19NUC4OC / Gene (production host): NUCA / Production host: Serratia marcescens (bacteria) / Strain (production host): PROTEASE DEFICIENT STRAIN / References: UniProt: P13717, Serratia marcescens nuclease
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsREFERENCE DATABASE: GENBANK ENTRY_NAME: SMANUCES

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: CRYSTALLIZATION METHOD: VAPOR DIFFUSION SITTING DROP CRYSTALLIZATION TEMPERATURE: 277 K CRYSTALLIZATION PH: 4.6 CRYSTALS WERE GROWN FROM PEG 3350, AMMONIUM SULFATE, SODIUM ACETATE, AND ...Details: CRYSTALLIZATION METHOD: VAPOR DIFFUSION SITTING DROP CRYSTALLIZATION TEMPERATURE: 277 K CRYSTALLIZATION PH: 4.6 CRYSTALS WERE GROWN FROM PEG 3350, AMMONIUM SULFATE, SODIUM ACETATE, AND STORED IN A STABILIZATION SOLUTION CONTAINING 20% PEG 3000, 400mM GLYCINE, 40mM TRIS, PH8.2 (293 K), 20% PEG 3000, 10% PEG 400. THIS SOLUTION WAS EXCHANGED THREE TIMES TO MINIMIZE CARRY OVER FROM THE STORAGE SOLUTION. AFTER 3 DAYS IN THE MAGNESIUM STABILIZATION SOLUTION, THE CRYSTAL OF DIMENSION 0.4 X 0.4 X 0.3 MM**2 WAS MOUNTED IN A SILICONIZED SPECIAL GLASS CAPILLARY. , VAPOR DIFFUSION, SITTING DROP
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 4.6 / Method: other
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 %(w/v)PEG335011
20.2 Mammonium sulfate11
30.1 Msodium acetate11

-
Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Feb 2, 1998
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→45 Å / Num. obs: 30574 / % possible obs: 84.3 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 6.6 Å2 / Rmerge(I) obs: 0.025 / Net I/σ(I): 40.87
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.045 / Mean I/σ(I) obs: 18.9 / % possible all: 20.4
Reflection
*PLUS
Num. measured all: 93785

-
Processing

Software
NameVersionClassification
MADNESSdata collection
PROCORdata scaling
PROCORdata reduction
XSCALEdata scaling
ARP/wARPmodel building
X-PLOR3.851model building
X-PLOR3.851refinement
MADNESSdata reduction
X-PLOR3.851phasing
RefinementStarting model: 1.4 ANGSTROM STRUCTURE OF THE SERRATIAL ENDONUCLEASE (CAI, MILLER AND KRAUSE) WITH WATER AND ALTERNATE SIDE CHAIN CONFORMERS REMOVED AND THE SIDE CHAINS FOR THE ACTIVE SITE RESIDUES ...Starting model: 1.4 ANGSTROM STRUCTURE OF THE SERRATIAL ENDONUCLEASE (CAI, MILLER AND KRAUSE) WITH WATER AND ALTERNATE SIDE CHAIN CONFORMERS REMOVED AND THE SIDE CHAINS FOR THE ACTIVE SITE RESIDUES ARG 57, HIS 89, ASN 199 AND GLU 127 OMITTED

Resolution: 2.05→50 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: BULK SOLVENT MODEL USED, NCS B-FACTORS RESTRAINTS WERE APPLIED TO PROTEIN ATOMS AND PAIRS OF WATER MOLECULES WHICH DEVIATED LESS THAN 1.0 ANGSTROMS FROM NCS. THE PROTEIN ATOMS ARE IN GROUP 1 ...Details: BULK SOLVENT MODEL USED, NCS B-FACTORS RESTRAINTS WERE APPLIED TO PROTEIN ATOMS AND PAIRS OF WATER MOLECULES WHICH DEVIATED LESS THAN 1.0 ANGSTROMS FROM NCS. THE PROTEIN ATOMS ARE IN GROUP 1 AND THE WATER IS IN GROUP 2. WATER HOH 1 SITS ON THE NON-CRYSTALLOGRAPHIC 2-FOLD AXIS AND IT IS ITS OWN NCS MATE. THE WATER PAIRS IN GROUP 2 BEGIN WITH (HOH 2,HOH 3) AND END WITH (HOH 188, HOH 189). WATERS HOH 190 TO HOH 241 DO NOT HAVE NCS MATES WITHIN 1.0 ANGSTROMS. CRYST1 THERE IS STRONG PSEUDO-CENTERING ARISING FROM THE NON-CRYSTALLOGRAPHIC SYMMETRY. SHIFTING ONE MONOMER BY ONLY 1.4 ANGSTROMS WITH A 1 DEGREE ROTATION WOULD CHANGE THE SPACE GROUP TO I 2 2 2.
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1483 5.1 %RANDOM
Rwork0.167 ---
obs-29209 83 %-
Displacement parametersBiso mean: 14.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3690 0 2 251 3943
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.61
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.121.5
X-RAY DIFFRACTIONx_mcangle_it1.832
X-RAY DIFFRACTIONx_scbond_it2.322.25
X-RAY DIFFRACTIONx_scangle_it3.532.5
Refine LS restraints NCS
Ens-IDDom-IDRefine-IDRms dev Biso (Å2)Weight Biso
11X-RAY DIFFRACTION0.7821
22X-RAY DIFFRACTION0.2750.3
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.21 122 4.3 %
Rwork0.192 2728 -
obs--49.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.SOL
Software
*PLUS
Name: X-PLOR(ONLINE) / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.167 / Rfactor Rfree: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.61
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5

+
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://pdbjlvh1.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