[English] 日本語
Yorodumi
- PDB-4qrn: HIGH-RESOLUTION CRYSTAL STRUCTURE of 5-CARBOXYVANILLATE DECARBOXY... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qrn
TitleHIGH-RESOLUTION CRYSTAL STRUCTURE of 5-CARBOXYVANILLATE DECARBOXYLASE (TARGET EFI-505250) FROM NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 COMPLEXED WITH MANGANESE AND 4-HYDROXY-3-METHOXY-5-NITROBENZOIC ACID
Components5-Carboxyvanillate Decarboxylase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / DECARBOXYLASE / ENZYME FUNCTION INITIATIVE / EFI / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


organic substance metabolic process / carboxy-lyase activity / hydrolase activity / metal ion binding
Similarity search - Function
2-amino-3-carboxymuconate-6-semialdehyde decarboxylase / Amidohydrolase / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
4-hydroxy-3-methoxy-5-nitrobenzoic acid / ACETATE ION / : / Amidohydrolase 2
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å
AuthorsPatskovsky, Y. / Vladimirova, A. / Toro, R. / Bhosle, R. / Gerlt, J.A. / Raushel, F.M. / Almo, S.C.
CitationJournal: To be Published
Title: Crystal Structure of 5-Carboxyvanillate Decarboxylase from Novosphingobium Aromaticivorans
Authors: Patskovsky, Y. / Vladimirova, A. / Toro, R. / Bhosle, R. / Raushel, F.M. / Almo, S.C.
History
DepositionJul 1, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionAug 6, 2014ID: 4ING
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: 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_ref_seq_dif / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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_ref_seq_dif.details / _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: 5-Carboxyvanillate Decarboxylase
B: 5-Carboxyvanillate Decarboxylase
C: 5-Carboxyvanillate Decarboxylase
D: 5-Carboxyvanillate Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,79327
Polymers169,8254
Non-polymers1,96823
Water36,1202005
1
A: 5-Carboxyvanillate Decarboxylase
B: 5-Carboxyvanillate Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,92614
Polymers84,9132
Non-polymers1,01312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7720 Å2
ΔGint-106 kcal/mol
Surface area23510 Å2
MethodPISA
2
C: 5-Carboxyvanillate Decarboxylase
D: 5-Carboxyvanillate Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,86713
Polymers84,9132
Non-polymers95411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7460 Å2
ΔGint-102 kcal/mol
Surface area23240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.723, 60.747, 130.517
Angle α, β, γ (deg.)90.00, 103.33, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
5-Carboxyvanillate Decarboxylase


Mass: 42456.277 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria)
Strain: DSM 12444 / F199 / Gene: Saro_0799 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2GA79

-
Non-polymers , 6 types, 2028 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-1DF / 4-hydroxy-3-methoxy-5-nitrobenzoic acid


Mass: 213.144 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H7NO6
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2005 / 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: 2.11 Å3/Da / Density % sol: 41.6 %
Crystal growpH: 8.5
Details: 0.085M TRIS-HCL, PH 8.5, 0.17M SODIUM ACETATE, 25% PEG 4000,15% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.92
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 24, 2014 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.068→50 Å / Num. obs: 614492 / % possible obs: 98.9 % / Observed criterion σ(I): -5 / Redundancy: 3.5 % / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 9.8
Reflection shellResolution: 1.07→1.09 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2 / Rsym value: 0.65 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DVT

2dvt


Resolution: 1.07→28.14 Å / SU ML: 0.08 / σ(F): 1.34 / Phase error: 15.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.155 12447 2.03 %
Rwork0.135 --
obs0.136 614348 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.07→28.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11134 0 112 2005 13251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111948
X-RAY DIFFRACTIONf_angle_d1.46816217
X-RAY DIFFRACTIONf_dihedral_angle_d13.3334594
X-RAY DIFFRACTIONf_chiral_restr0.0841710
X-RAY DIFFRACTIONf_plane_restr0.012135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0684-1.08060.26013910.255119464X-RAY DIFFRACTION96
1.0806-1.09330.2293940.224520196X-RAY DIFFRACTION100
1.0933-1.10660.21814130.202220245X-RAY DIFFRACTION100
1.1066-1.12060.19144090.191320172X-RAY DIFFRACTION100
1.1206-1.13540.21154240.176320130X-RAY DIFFRACTION100
1.1354-1.15090.17453860.164620249X-RAY DIFFRACTION100
1.1509-1.16740.18634430.152220218X-RAY DIFFRACTION100
1.1674-1.18480.16044220.145420079X-RAY DIFFRACTION100
1.1848-1.20330.15884260.142920265X-RAY DIFFRACTION100
1.2033-1.2230.16974610.140120095X-RAY DIFFRACTION100
1.223-1.24410.16114230.135420210X-RAY DIFFRACTION100
1.2441-1.26670.14934020.127120192X-RAY DIFFRACTION100
1.2667-1.29110.13323820.125920234X-RAY DIFFRACTION100
1.2911-1.31750.15624320.124720226X-RAY DIFFRACTION100
1.3175-1.34610.16024110.125120210X-RAY DIFFRACTION100
1.3461-1.37740.14724420.118420177X-RAY DIFFRACTION100
1.3774-1.41190.13734170.114720305X-RAY DIFFRACTION100
1.4119-1.450.14993860.114520239X-RAY DIFFRACTION100
1.45-1.49270.13784190.112520207X-RAY DIFFRACTION100
1.4927-1.54090.12874620.106620302X-RAY DIFFRACTION100
1.5409-1.59590.13284170.10620271X-RAY DIFFRACTION100
1.5959-1.65980.13024180.106220253X-RAY DIFFRACTION100
1.6598-1.73540.13883900.114220385X-RAY DIFFRACTION100
1.7354-1.82680.14164100.12320262X-RAY DIFFRACTION100
1.8268-1.94130.1464370.125820339X-RAY DIFFRACTION100
1.9413-2.09110.1354280.121220377X-RAY DIFFRACTION100
2.0911-2.30150.14144040.124520377X-RAY DIFFRACTION100
2.3015-2.63430.15274330.134920427X-RAY DIFFRACTION100
2.6343-3.31810.16544140.145519766X-RAY DIFFRACTION96
3.3181-28.14820.17643510.168116029X-RAY DIFFRACTION77

+
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