[English] 日本語
Yorodumi
- PDB-3pci: STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 3-IOD... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pci
TitleSTRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 3-IODO-4-HYDROXYBENZOATE
Components(PROTOCATECHUATE 3,4- ...) x 2
KeywordsDIOXYGENASE / IRON / NONHEME / METALLOPROTEIN / OXIDOREDUCTASE / INHIBITOR COMPLEX
Function / homology
Function and homology information


protocatechuate 3,4-dioxygenase / protocatechuate 3,4-dioxygenase activity / 3,4-dihydroxybenzoate catabolic process / beta-ketoadipate pathway / ferric iron binding
Similarity search - Function
Protocatechuate 3,4-dioxygenase, beta subunit / Protocatechuate 3,4-dioxygenase, alpha subunit / Protocatechuate 3,4-dioxygenase beta subunit, N-terminal / Protocatechuate 3,4-dioxygenase beta subunit N terminal / Protocatechuate 3,4-Dioxygenase, subunit A / Aromatic compound dioxygenase / Intradiol ring-cleavage dioxygenases signature. / : / Intradiol ring-cleavage dioxygenase, C-terminal / Intradiol ring-cleavage dioxygenase, core ...Protocatechuate 3,4-dioxygenase, beta subunit / Protocatechuate 3,4-dioxygenase, alpha subunit / Protocatechuate 3,4-dioxygenase beta subunit, N-terminal / Protocatechuate 3,4-dioxygenase beta subunit N terminal / Protocatechuate 3,4-Dioxygenase, subunit A / Aromatic compound dioxygenase / Intradiol ring-cleavage dioxygenases signature. / : / Intradiol ring-cleavage dioxygenase, C-terminal / Intradiol ring-cleavage dioxygenase, core / Dioxygenase / Sandwich / Mainly Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / : / 3-IODO-4-HYDROXYBENZOIC ACID / Protocatechuate 3,4-dioxygenase alpha chain / Protocatechuate 3,4-dioxygenase beta chain
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / NATIVE MODEL PHASES / Resolution: 2.21 Å
AuthorsOrville, A.M. / Elango, N. / Lipscomb, J.D. / Ohlendorf, D.H.
Citation
Journal: Biochemistry / Year: 1997
Title: Structures of competitive inhibitor complexes of protocatechuate 3,4-dioxygenase: multiple exogenous ligand binding orientations within the active site.
Authors: Orville, A.M. / Elango, N. / Lipscomb, J.D. / Ohlendorf, D.H.
#1: Journal: Biochemistry / Year: 1997
Title: Crystal Structures of Substrate and Substrate Analog Complexes of Protocatechuate 3,4-Dioxygenase: Endogenous Fe3+ Ligand Displacement in Response to Substrate Binding
Authors: Orville, A.M. / Lipscomb, J.D. / Ohlendorf, D.H.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: Structure of Protocatechuate 3,4-Dioxygenase from Pseudomonas Aeruginosa at 2.15 A Resolution
Authors: Ohlendorf, D.H. / Orville, A.M. / Lipscomb, J.D.
#3: Journal: Nature / Year: 1988
Title: Structure and Assembly of Protocatechuate 3,4-Dioxygenase
Authors: Ohlendorf, D.H. / Lipscomb, J.D. / Weber, P.C.
History
DepositionJul 2, 1997Processing site: BNL
Revision 1.0Jan 21, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 2.0Sep 27, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / atom_sites ...atom_site / atom_sites / chem_comp_atom / chem_comp_bond / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_database_status / pdbx_struct_conn_angle / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conn / struct_ncs_oper / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_z ..._atom_site.Cartn_x / _atom_site.Cartn_z / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[3][1] / _atom_sites.fract_transf_matrix[3][3] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][3] / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTOCATECHUATE 3,4-DIOXYGENASE
M: PROTOCATECHUATE 3,4-DIOXYGENASE
B: PROTOCATECHUATE 3,4-DIOXYGENASE
N: PROTOCATECHUATE 3,4-DIOXYGENASE
C: PROTOCATECHUATE 3,4-DIOXYGENASE
O: PROTOCATECHUATE 3,4-DIOXYGENASE
D: PROTOCATECHUATE 3,4-DIOXYGENASE
P: PROTOCATECHUATE 3,4-DIOXYGENASE
E: PROTOCATECHUATE 3,4-DIOXYGENASE
Q: PROTOCATECHUATE 3,4-DIOXYGENASE
F: PROTOCATECHUATE 3,4-DIOXYGENASE
R: PROTOCATECHUATE 3,4-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,82336
Polymers293,85112
Non-polymers3,97224
Water26,5901476
1
A: PROTOCATECHUATE 3,4-DIOXYGENASE
M: PROTOCATECHUATE 3,4-DIOXYGENASE
B: PROTOCATECHUATE 3,4-DIOXYGENASE
N: PROTOCATECHUATE 3,4-DIOXYGENASE
C: PROTOCATECHUATE 3,4-DIOXYGENASE
O: PROTOCATECHUATE 3,4-DIOXYGENASE
D: PROTOCATECHUATE 3,4-DIOXYGENASE
P: PROTOCATECHUATE 3,4-DIOXYGENASE
E: PROTOCATECHUATE 3,4-DIOXYGENASE
Q: PROTOCATECHUATE 3,4-DIOXYGENASE
F: PROTOCATECHUATE 3,4-DIOXYGENASE
R: PROTOCATECHUATE 3,4-DIOXYGENASE
hetero molecules

A: PROTOCATECHUATE 3,4-DIOXYGENASE
M: PROTOCATECHUATE 3,4-DIOXYGENASE
B: PROTOCATECHUATE 3,4-DIOXYGENASE
N: PROTOCATECHUATE 3,4-DIOXYGENASE
C: PROTOCATECHUATE 3,4-DIOXYGENASE
O: PROTOCATECHUATE 3,4-DIOXYGENASE
D: PROTOCATECHUATE 3,4-DIOXYGENASE
P: PROTOCATECHUATE 3,4-DIOXYGENASE
E: PROTOCATECHUATE 3,4-DIOXYGENASE
Q: PROTOCATECHUATE 3,4-DIOXYGENASE
F: PROTOCATECHUATE 3,4-DIOXYGENASE
R: PROTOCATECHUATE 3,4-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)595,64572
Polymers587,70124
Non-polymers7,94448
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x+1/2,y-1/2,-z+1/21
2
A: PROTOCATECHUATE 3,4-DIOXYGENASE
M: PROTOCATECHUATE 3,4-DIOXYGENASE
B: PROTOCATECHUATE 3,4-DIOXYGENASE
N: PROTOCATECHUATE 3,4-DIOXYGENASE
C: PROTOCATECHUATE 3,4-DIOXYGENASE
O: PROTOCATECHUATE 3,4-DIOXYGENASE
D: PROTOCATECHUATE 3,4-DIOXYGENASE
P: PROTOCATECHUATE 3,4-DIOXYGENASE
E: PROTOCATECHUATE 3,4-DIOXYGENASE
Q: PROTOCATECHUATE 3,4-DIOXYGENASE
F: PROTOCATECHUATE 3,4-DIOXYGENASE
R: PROTOCATECHUATE 3,4-DIOXYGENASE
hetero molecules

A: PROTOCATECHUATE 3,4-DIOXYGENASE
M: PROTOCATECHUATE 3,4-DIOXYGENASE
B: PROTOCATECHUATE 3,4-DIOXYGENASE
N: PROTOCATECHUATE 3,4-DIOXYGENASE
C: PROTOCATECHUATE 3,4-DIOXYGENASE
O: PROTOCATECHUATE 3,4-DIOXYGENASE
D: PROTOCATECHUATE 3,4-DIOXYGENASE
P: PROTOCATECHUATE 3,4-DIOXYGENASE
E: PROTOCATECHUATE 3,4-DIOXYGENASE
Q: PROTOCATECHUATE 3,4-DIOXYGENASE
F: PROTOCATECHUATE 3,4-DIOXYGENASE
R: PROTOCATECHUATE 3,4-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)595,64572
Polymers587,70124
Non-polymers7,94448
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area144410 Å2
ΔGint-760 kcal/mol
Surface area163480 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)197.000, 127.070, 134.080
Angle α, β, γ (deg.)90.00, 97.53, 90.00
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(0.2084611, 0.97381411, -0.04588354), (0.24334334, 0.97418598), (0.94709405, -0.24325045, -0.20846109)
2given(0.23697118, 0.21416355, 0.94867605), (0.97337337, -0.21424533), (-0.05919338, 0.97300181, -0.23697118)
3given(-0.89576945, 0.41727025), (-1), (0.47354702, 0.89576945)
4given(0.2084611, -0.97381411, -0.04588354), (-0.24334334, -0.97418598), (0.94709405, 0.24325045, -0.20846109)
5given(-0.23697118, 0.21416355, -0.94867605), (-0.97337337, 0.21424533), (0.05919338, 0.97300181, 0.23697118)
DetailsTHE ACTIVE FORM OF THE ENZYME IS THE WHOLE UNIT CELL CONTENT. IT CONSISTS OF 12 PROTOMERS. EACH PROTOMER IS MADE OF TWO POLYPEPTIDE CHAINS AND ONE FE(III). THE ASYMMETRIC UNIT CONSISTS OF 6 PROTOMERS. THEY ARE: CHAINS (A, M), CHAINS (B, N), CHAINS (C, O), CHAINS (D, P), CHAINS (E, Q), CHAINS (F, R). EACH PROTOMER CONTAINS AN ACTIVE SITE WITH FE(III) AS THE CENTER AND A VESTIGIAL SITE. THE ACTIVE SITES ARE NAMED: ACA, ACB, ACC, ACD, ACE, ACF. THE VESTIGIAL SITES ARE NAMED VEA, VEB, VEC, VED, VEE AND VEF. THE CHAIN IDENTIFIERS HAVE BEEN ASSIGNED AS FOLLOWS: ALPHA BETA WATERS A M G B N H C O I D P J E Q K F R L

-
Components

-
PROTOCATECHUATE 3,4- ... , 2 types, 12 molecules ABCDEFMNOPQR

#1: Protein
PROTOCATECHUATE 3,4-DIOXYGENASE


Mass: 22278.812 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: PREVIOUSLY CLASSIFIED AS PSEUDOMONAS AERUGINOSA / Source: (natural) Pseudomonas putida (bacteria)
References: UniProt: P00436, protocatechuate 3,4-dioxygenase
#2: Protein
PROTOCATECHUATE 3,4-DIOXYGENASE


Mass: 26696.287 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: PREVIOUSLY CLASSIFIED AS PSEUDOMONAS AERUGINOSA / Source: (natural) Pseudomonas putida (bacteria)
References: UniProt: P00437, protocatechuate 3,4-dioxygenase

-
Non-polymers , 4 types, 1500 molecules

#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical
ChemComp-IHB / 3-IODO-4-HYDROXYBENZOIC ACID


Mass: 264.017 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C7H5IO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1476 / Source method: isolated from a natural source / Formula: H2O

-
Details

Nonpolymer detailsTHE INHIBITOR IS OBSERVED IN TWO BINDING SITES. THE FIRST IS IN THE ACTIVE SITE OF EACH PROTOMER ...THE INHIBITOR IS OBSERVED IN TWO BINDING SITES. THE FIRST IS IN THE ACTIVE SITE OF EACH PROTOMER (RESIDUE 550). THE SECOND IS AT EACH LOCAL THREE-FOLD SYMMETRY AXIS (RESIDUE 551). THE SECONDARY BINDING SITES ARE DEFINED BY: S2M AND S2P.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.52 %
Crystal growpH: 8.4 / Details: pH 8.4
Crystal grow
*PLUS
Method: interface diffusion / Details: or hanging drop vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120-75 mg/mlprotein1drop
21.5-1.8 Mammonium sulfate1reservoir
350 mMTris-HCl1reservoir
410 mMbeta-mercaptoethanol1reservoir

-
Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Feb 5, 1992 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.21→10 Å / Num. obs: 135334 / % possible obs: 83 % / Observed criterion σ(I): 1 / Redundancy: 1.61 % / Rsym value: 0.055 / Net I/σ(I): 14.32
Reflection shellResolution: 2.21→2.35 Å / Redundancy: 1.2 % / Mean I/σ(I) obs: 1.3 / % possible all: 43
Reflection
*PLUS
Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 43 %

-
Processing

Software
NameClassification
PROLSQrefinement
XENGENdata reduction
XENGENdata scaling
RefinementMethod to determine structure: NATIVE MODEL PHASES / Resolution: 2.21→6 Å / σ(F): 1
Details: THE NONSTANDARD UNIT CELL I 2 WAS CHOSEN OVER THE EQUIVALENT C 2 CELL BECAUSE OF THE CONVENIENCE OF HAVING A BETA ANGLE NEAR 90 DEGREES AND TO MAINTAIN CONSISTENCY WITH THE INITIAL ...Details: THE NONSTANDARD UNIT CELL I 2 WAS CHOSEN OVER THE EQUIVALENT C 2 CELL BECAUSE OF THE CONVENIENCE OF HAVING A BETA ANGLE NEAR 90 DEGREES AND TO MAINTAIN CONSISTENCY WITH THE INITIAL CRYSTALLIZATION REPORT. TO CONVERT FROM FRACTIONAL I 2 TO FRACTIONAL C 2, USE THE FOLLOWING TRANSFORMATION: [ 1.0 ][ 0.0 ][ 0.0 ] (XFRAC_I2) (XFRAC_C2) [ 0.0 ][ 1.0 ][ 0.0 ] X (YFRAC_I2) = (YFRAC_C2) [ -1.0 ][ 0.0 ][ 1.0 ] (ZFRAC_I2) (ZFRAC_C2) THE ORTHOGONAL COORDINATE SYSTEM CHOSEN FOR THIS ENTRY IS THAT DEFINED BY THE LOCAL SYMMETRY OF THE COMPLEX (23).
RfactorNum. reflection% reflection
Rwork0.159 --
obs-113850 83 %
Displacement parametersBiso mean: 22.94 Å2
Refinement stepCycle: LAST / Resolution: 2.21→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20466 0 162 1476 22104
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.03
X-RAY DIFFRACTIONp_angle_d0.0290.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0290.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.5261
X-RAY DIFFRACTIONp_mcangle_it0.9452
X-RAY DIFFRACTIONp_scbond_it1.0481.5
X-RAY DIFFRACTIONp_scangle_it1.753
X-RAY DIFFRACTIONp_plane_restr0.0120.03
X-RAY DIFFRACTIONp_chiral_restr0.2210.3
X-RAY DIFFRACTIONp_singtor_nbd0.1780.5
X-RAY DIFFRACTIONp_multtor_nbd0.210.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.170.5
X-RAY DIFFRACTIONp_planar_tor23
X-RAY DIFFRACTIONp_staggered_tor1715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor23.320
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.159
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / Rfactor obs: 0.212

+
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