[English] 日本語
Yorodumi
- PDB-1rz1: Reduced flavin reductase PheA2 in complex with NAD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rz1
TitleReduced flavin reductase PheA2 in complex with NAD
Componentsphenol 2-hydroxylase component B
KeywordsOXIDOREDUCTASE / flavin / NAD
Function / homology
Function and homology information


pyrimidine nucleobase catabolic process / riboflavin reductase (NADPH) activity / FMN binding
Similarity search - Function
: / Flavin reductase like domain / Flavin reductase like domain / Flavin reductase like domain / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Phenol 2-hydroxylase component B
Similarity search - Component
Biological speciesGeobacillus thermoglucosidasius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsVan Den Heuvel, R.H. / Westphal, A.H. / Heck, A.J. / Walsh, M.A. / Rovida, S. / Van Berkel, W.J. / Mattevi, A.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural Studies on Flavin Reductase PheA2 Reveal Binding of NAD in an Unusual Folded Conformation and Support Novel Mechanism of Action.
Authors: Van Den Heuvel, R.H. / Westphal, A.H. / Heck, A.J. / Walsh, M.A. / Rovida, S. / Van Berkel, W.J. / Mattevi, A.
History
DepositionDec 23, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 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 / struct_conn / struct_ncs_dom_lim / 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_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: phenol 2-hydroxylase component B
B: phenol 2-hydroxylase component B
C: phenol 2-hydroxylase component B
D: phenol 2-hydroxylase component B
E: phenol 2-hydroxylase component B
F: phenol 2-hydroxylase component B
G: phenol 2-hydroxylase component B
H: phenol 2-hydroxylase component B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,25324
Polymers143,6618
Non-polymers11,59216
Water7,152397
1
A: phenol 2-hydroxylase component B
B: phenol 2-hydroxylase component B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8136
Polymers35,9152
Non-polymers2,8984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9470 Å2
ΔGint-65 kcal/mol
Surface area12480 Å2
MethodPISA
2
C: phenol 2-hydroxylase component B
D: phenol 2-hydroxylase component B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8136
Polymers35,9152
Non-polymers2,8984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9500 Å2
ΔGint-65 kcal/mol
Surface area12420 Å2
MethodPISA
3
E: phenol 2-hydroxylase component B
F: phenol 2-hydroxylase component B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8136
Polymers35,9152
Non-polymers2,8984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9510 Å2
ΔGint-65 kcal/mol
Surface area12470 Å2
MethodPISA
4
G: phenol 2-hydroxylase component B
H: phenol 2-hydroxylase component B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8136
Polymers35,9152
Non-polymers2,8984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9490 Å2
ΔGint-65 kcal/mol
Surface area12480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.693, 156.457, 83.925
Angle α, β, γ (deg.)90.00, 91.11, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91A
101B
111C
121D
131E
141F
151G
161H
171A
181B
191C
201D
211E
221F
231G
241H
251A
261B
271C
281D
291E
301F
311G
321H

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPLEULEUAA3 - 243 - 24
21ASPASPLEULEUBB3 - 243 - 24
31ASPASPLEULEUCC3 - 243 - 24
41ASPASPLEULEUDD3 - 243 - 24
51ASPASPLEULEUEE3 - 243 - 24
61ASPASPLEULEUFF3 - 243 - 24
71ASPASPLEULEUGG3 - 243 - 24
81ASPASPLEULEUHH3 - 243 - 24
92ALAALAGLNGLNAA27 - 15327 - 153
102ALAALAGLNGLNBB27 - 15327 - 153
112ALAALAGLNGLNCC27 - 15327 - 153
122ALAALAGLNGLNDD27 - 15327 - 153
132ALAALAGLNGLNEE27 - 15327 - 153
142ALAALAGLNGLNFF27 - 15327 - 153
152ALAALAGLNGLNGG27 - 15327 - 153
162ALAALAGLNGLNHH27 - 15327 - 153
173FADFADFADFADAI1200
183FADFADFADFADBK2200
193FADFADFADFADCM3200
203FADFADFADFADDO4200
213FADFADFADFADEQ5200
223FADFADFADFADFS6200
233FADFADFADFADGU7200
243FADFADFADFADHW8200
254NADNADNADNADAJ1201
264NADNADNADNADBL2201
274NADNADNADNADCN3201
284NADNADNADNADDP4201
294NADNADNADNADER5201
304NADNADNADNADFT6201
314NADNADNADNADGV7201
324NADNADNADNADHX8201

-
Components

#1: Protein
phenol 2-hydroxylase component B / Flavin reductase PheA2


Mass: 17957.650 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermoglucosidasius (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: Q9LAG2
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.38 Å3/Da / Density % sol: 47.9 %

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 20, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→15 Å / Num. all: 80392 / Num. obs: 77418 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1RZ0

1rz0


Resolution: 2.1→15 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.968 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.291 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25604 1560 2 %RANDOM
Rwork0.23686 ---
all0.23726 0 --
obs0.23726 74830 95.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.413 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å20 Å2-0.6 Å2
2--1.06 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9408 0 776 397 10581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02210384
X-RAY DIFFRACTIONr_angle_refined_deg1.4892.05814152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.54751216
X-RAY DIFFRACTIONr_chiral_restr0.0910.21640
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027320
X-RAY DIFFRACTIONr_nbd_refined0.210.24609
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2539
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5490.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4260.29
X-RAY DIFFRACTIONr_mcbond_it0.8181.56056
X-RAY DIFFRACTIONr_mcangle_it1.60429760
X-RAY DIFFRACTIONr_scbond_it2.3834328
X-RAY DIFFRACTIONr_scangle_it3.8184.54392
Refine LS restraints NCS

Ens-ID: 1 / Number: 1245 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.040.05
2Btight positional0.050.05
3Ctight positional0.040.05
4Dtight positional0.050.05
5Etight positional0.040.05
6Ftight positional0.050.05
7Gtight positional0.040.05
8Htight positional0.050.05
1Atight thermal0.150.5
2Btight thermal0.170.5
3Ctight thermal0.160.5
4Dtight thermal0.140.5
5Etight thermal0.140.5
6Ftight thermal0.160.5
7Gtight thermal0.140.5
8Htight thermal0.170.5
LS refinement shellResolution: 2.1→2.153 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.346 111
Rwork0.357 4914

+
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