[English] 日本語
Yorodumi
- PDB-3qj4: Crystal structure of Human Renalase (isoform 1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qj4
TitleCrystal structure of Human Renalase (isoform 1)
ComponentsRenalase
KeywordsOXIDOREDUCTASE / FAD/NAD(P)-binding Rossmann fold Superfamily / Flavin containing amine oxidoreductase / Monoamine oxidase / NAD / extracellular
Function / homology
Function and homology information


renalase / epinephrine binding / monoamine oxidase activity / response to epinephrine / NAD biosynthesis via nicotinamide riboside salvage pathway / NADH binding / : / response to salt / Nicotinamide salvaging / oxidoreductase activity, acting on NAD(P)H ...renalase / epinephrine binding / monoamine oxidase activity / response to epinephrine / NAD biosynthesis via nicotinamide riboside salvage pathway / NADH binding / : / response to salt / Nicotinamide salvaging / oxidoreductase activity, acting on NAD(P)H / negative regulation of heart rate / negative regulation of blood pressure / response to ischemia / extracellular space / extracellular region
Similarity search - Function
Renalase / NAD(P)-binding Rossmann-like domain / Polyamine Oxidase; Chain A, domain 2 - #10 / Polyamine Oxidase; Chain A, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily ...Renalase / NAD(P)-binding Rossmann-like domain / Polyamine Oxidase; Chain A, domain 2 - #10 / Polyamine Oxidase; Chain A, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Renalase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMilani, M. / Ciriello, F. / Baroni, S. / Pandini, V. / Aliverti, A. / Canevari, G. / Bolognesi, M.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: FAD-binding site and NADP reactivity in human renalase: a new enzyme involved in blood pressure regulation
Authors: Milani, M. / Ciriello, F. / Baroni, S. / Pandini, V. / Canevari, G. / Bolognesi, M. / Aliverti, A.
History
DepositionJan 28, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Renalase
B: Renalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6027
Polymers75,7422
Non-polymers1,8595
Water2,306128
1
A: Renalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8494
Polymers37,8711
Non-polymers9783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Renalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7533
Polymers37,8711
Non-polymers8822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.837, 86.593, 93.180
Angle α, β, γ (deg.)90.00, 95.30, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Renalase / / Monoamine oxidase-C / MAO-C


Mass: 37871.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNLS / Plasmid: pET SUMO / Production host: Escherichia coli (E. coli)
References: UniProt: Q5VYX0, Oxidoreductases; Acting on the CH-NH2 group of donors
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNATURAL VARIANT, SEE UNP DATABASE RNLS_HUMAN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG 8000, 0.2M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 29, 2010
RadiationMonochromator: horizontally side diffracting Silicon 111 crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.5→48.39 Å / Num. all: 25082 / Num. obs: 29646 / % possible obs: 84.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 45.16 Å2
Reflection shellResolution: 2.5→2.64 Å / Num. possible: 3770

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
MOLREPphasing
BUSTER2.9.2refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KKJ

3kkj


Resolution: 2.5→28.94 Å / Cor.coef. Fo:Fc: 0.9218 / Cor.coef. Fo:Fc free: 0.8859 / Occupancy max: 1 / Occupancy min: 0.01 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2602 1284 5.14 %RANDOM
Rwork0.2169 ---
all0.2192 29510 --
obs0.2192 24995 --
Displacement parametersBiso max: 136.11 Å2 / Biso mean: 52.77 Å2 / Biso min: 18.02 Å2
Baniso -1Baniso -2Baniso -3
1-10.3297 Å20 Å2-3.1899 Å2
2---17.8108 Å20 Å2
3---7.4811 Å2
Refine analyzeLuzzati coordinate error obs: 0.369 Å
Refinement stepCycle: LAST / Resolution: 2.5→28.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5181 0 121 128 5430
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1866SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes155HARMONIC2
X-RAY DIFFRACTIONt_gen_planes812HARMONIC5
X-RAY DIFFRACTIONt_it5444HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion18HARMONIC0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion708SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5632SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5444HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg7411HARMONIC21.14
X-RAY DIFFRACTIONt_omega_torsion2.53
X-RAY DIFFRACTIONt_other_torsion22.59
LS refinement shellResolution: 2.5→2.6 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2657 137 4.76 %
Rwork0.223 2739 -
all0.225 2876 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.8253-0.2547-0.62860.82660.68983.2044-0.0777-0.0395-0.0212-0.06610.07260.0077-0.10.26610.0050.08670.02360.00030.04130.03810.141214.5045-6.468920.885
23.0485-0.3076-0.31470.8660.50922.7339-0.0627-0.4608-0.0713-0.09130.142-0.043-0.10710.0674-0.07930.06960.00710.00570.26330.0940.086329.566236.905126.7451
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth seq-ID
1X-RAY DIFFRACTION1A 1 - A 341, A 4010
2X-RAY DIFFRACTION2B 2 - B 341, B 4010

+
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