[English] 日本語
Yorodumi
- PDB-3bm7: CRYSTAL STRUCTURE OF A PUTATIVE ANTIBIOTIC BIOSYNTHESIS MONOOXYGE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bm7
TitleCRYSTAL STRUCTURE OF A PUTATIVE ANTIBIOTIC BIOSYNTHESIS MONOOXYGENASE (CC_2132) FROM CAULOBACTER CRESCENTUS CB15 AT 1.35 A RESOLUTION
ComponentsProtein of unknown function with ferredoxin-like fold
KeywordsOXIDOREDUCTASE / FERREDOXIN-LIKE FOLD / ANTIBIOTIC BIOSYNTHESIS MONOOXYGENASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


: / ABM domain profile. / Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ABM domain-containing protein
Similarity search - Component
Biological speciesCaulobacter crescentus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of protein of unknown function with ferredoxin-like fold (NP_420935.1) from Caulobacter crescentus at 1.35 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein of unknown function with ferredoxin-like fold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9333
Polymers12,8091
Non-polymers1242
Water2,180121
1
A: Protein of unknown function with ferredoxin-like fold
hetero molecules

A: Protein of unknown function with ferredoxin-like fold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8666
Polymers25,6182
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+3/21
Buried area2290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.780, 81.200, 46.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Protein of unknown function with ferredoxin-like fold


Mass: 12808.907 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus (bacteria) / Species: Caulobacter vibrioides / Strain: CB15 / Gene: NP_420935.1, CC_2132 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9A6G2
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: NANODROP, 1.0M LiCl, 10.0% PEG 6000, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97904 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 19, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionResolution: 1.35→25.777 Å / Num. obs: 25876 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.93 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 13.62
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.35-1.40.4561.860764965196.7
1.4-1.450.3412.565454463199.2
1.45-1.520.253.477415276199.2
1.52-1.60.1634.772394943199
1.6-1.70.0996.972414963199
1.7-1.830.08410.2103914875198.9
1.83-2.020.0615.7152595094199.2
2.02-2.310.0424.1183884912199
2.31-2.910.0331.5181714770196.1
2.91-25.7770.02337.6154824557190.9

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.35→25.777 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.689 / SU ML: 0.05 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.057
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. ETHYLENE GLYCOL MOLECULES FROM THE CRYSTALLIZATION CONDITIONS WERE MODELED. 5. THERE IS UNMODELED DENSITY NEAR GLN 40.
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1317 5.1 %RANDOM
Rwork0.189 ---
obs0.19 25860 98.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.442 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å20 Å20 Å2
2--2.12 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.35→25.777 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms793 0 8 121 922
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022872
X-RAY DIFFRACTIONr_bond_other_d0.0010.02558
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.961187
X-RAY DIFFRACTIONr_angle_other_deg0.9231378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3795117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.17925.14335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.24615138
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.293151
X-RAY DIFFRACTIONr_chiral_restr0.0930.2130
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021014
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02171
X-RAY DIFFRACTIONr_nbd_refined0.2210.2183
X-RAY DIFFRACTIONr_nbd_other0.1790.2536
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2435
X-RAY DIFFRACTIONr_nbtor_other0.0870.2429
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.289
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2870.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2290.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.216
X-RAY DIFFRACTIONr_mcbond_it2.0623601
X-RAY DIFFRACTIONr_mcbond_other0.4563228
X-RAY DIFFRACTIONr_mcangle_it2.525898
X-RAY DIFFRACTIONr_scbond_it4.3358337
X-RAY DIFFRACTIONr_scangle_it4.8611289
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 87 -
Rwork0.347 1804 -
all-1891 -
obs--98.39 %
Refinement TLS params.Method: refined / Origin x: 8.6547 Å / Origin y: 26.0183 Å / Origin z: 39.9787 Å
111213212223313233
T-0.0603 Å2-0.001 Å20.0042 Å2--0.0517 Å2-0.0107 Å2---0.0283 Å2
L1.5585 °2-0.3744 °20.4798 °2-1.1006 °2-0.278 °2--1.7524 °2
S0.0078 Å °-0.0118 Å °0.0304 Å °0.0574 Å °0.0177 Å °-0.1766 Å °-0.0139 Å °0.1299 Å °-0.0255 Å °

+
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