[English] 日本語
Yorodumi
- PDB-7er8: Crystal structure of human Biliverdin IX-beta reductase B with Su... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7er8
TitleCrystal structure of human Biliverdin IX-beta reductase B with Sulfasalazine (SAS)
ComponentsFlavin reductase (NADPH)
KeywordsOXIDOREDUCTASE / platelets / Biliverdin reductaseB / BLVRB / inhibitors / NADP / Sulfasalazine
Function / homology
Function and homology information


FMN reductase (NADH) activity / biliberdin reductase (NAD+) activity / biliverdin reductase (NADP+) activity / biliverdin reductase [NAD(P)+] activity / flavin reductase (NADPH) / FMN reductase (NAD(P)H) activity / FMN reductase (NADPH) activity / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity ...FMN reductase (NADH) activity / biliberdin reductase (NAD+) activity / biliverdin reductase (NADP+) activity / biliverdin reductase [NAD(P)+] activity / flavin reductase (NADPH) / FMN reductase (NAD(P)H) activity / FMN reductase (NADPH) activity / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / megakaryocyte differentiation / riboflavin reductase (NADPH) activity / heme catabolic process / Heme degradation / negative regulation of insulin receptor signaling pathway / Cytoprotection by HMOX1 / intracellular membrane-bounded organelle / extracellular exosome / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / NAD(P)H-binding / NAD(P)-binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-SAS / Flavin reductase (NADPH)
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsGriesinger, C. / Lee, D. / Ryu, K.S. / Kim, M. / Ha, J.H.
CitationJournal: J.Med.Chem. / Year: 2022
Title: Repositioning Food and Drug Administration-Approved Drugs for Inhibiting Biliverdin IX beta Reductase B as a Novel Thrombocytopenia Therapeutic Target.
Authors: Kim, M. / Ha, J.H. / Choi, J. / Kim, B.R. / Gapsys, V. / Lee, K.O. / Jee, J.G. / Chakrabarti, K.S. / de Groot, B.L. / Griesinger, C. / Ryu, K.S. / Lee, D.
History
DepositionMay 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Flavin reductase (NADPH)
B: Flavin reductase (NADPH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,82411
Polymers47,0602
Non-polymers2,7649
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-59 kcal/mol
Surface area16970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.160, 117.367, 41.606
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-552-

HOH

21A-664-

HOH

-
Components

#1: Protein Flavin reductase (NADPH) / FR / Biliverdin reductase B / BVR-B / Biliverdin-IX beta-reductase / Green heme-binding protein / ...FR / Biliverdin reductase B / BVR-B / Biliverdin-IX beta-reductase / Green heme-binding protein / GHBP / NADPH-dependent diaphorase / NADPH-flavin reductase / FLR


Mass: 23529.822 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BLVRB, FLR / Production host: Escherichia coli (E. coli)
References: UniProt: P30043, flavin reductase (NADPH), biliverdin reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SAS / 2-HYDROXY-(5-([4-(2-PYRIDINYLAMINO)SULFONYL]PHENYL)AZO)BENZOIC ACID / SULFASALAZINE


Mass: 398.393 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H14N4O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43.98 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.9-2.0M Ammonium sulfate, 0.1M Bis-tris (pH 6.5)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.446→50 Å / Num. obs: 72377 / % possible obs: 99.39 % / Redundancy: 9.8 % / Biso Wilson estimate: 14.04 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09682 / Net I/σ(I): 15.11
Reflection shellResolution: 1.446→1.498 Å / Rmerge(I) obs: 0.4523 / Num. unique obs: 6896 / CC1/2: 0.721

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-20001.16_3549data collection
HKL-20001.16_3549data scaling
PHENIXmodel building
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HE5

1he5


Resolution: 1.45→47.75 Å / SU ML: 0.1424 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 18.1207
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1991 2000 2.76 %
Rwork0.1655 70377 -
obs0.1664 72377 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.22 Å2
Refinement stepCycle: LAST / Resolution: 1.45→47.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3116 0 177 380 3673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01443395
X-RAY DIFFRACTIONf_angle_d1.46964659
X-RAY DIFFRACTIONf_chiral_restr0.1033536
X-RAY DIFFRACTIONf_plane_restr0.0089584
X-RAY DIFFRACTIONf_dihedral_angle_d9.56991895
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.480.25631330.24464673X-RAY DIFFRACTION93.89
1.48-1.520.22081410.22274977X-RAY DIFFRACTION99.46
1.52-1.570.22991410.2074940X-RAY DIFFRACTION99.39
1.57-1.620.24181420.19435020X-RAY DIFFRACTION99.73
1.62-1.670.21781420.1834984X-RAY DIFFRACTION99.77
1.67-1.740.22951420.1794993X-RAY DIFFRACTION99.69
1.74-1.820.18911420.16955013X-RAY DIFFRACTION99.56
1.82-1.920.19891430.16435017X-RAY DIFFRACTION99.71
1.92-2.040.20311430.15975012X-RAY DIFFRACTION99.9
2.04-2.190.19841440.15925082X-RAY DIFFRACTION99.83
2.19-2.420.20771430.15395042X-RAY DIFFRACTION99.79
2.42-2.770.18491460.16755124X-RAY DIFFRACTION99.94
2.77-3.480.18771450.16175129X-RAY DIFFRACTION99.75
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)
12.546654194770.6930448283770.2993057882632.81374027161-0.1719302032621.836626234690.07649658401530.4097918408230.376858322606-0.1649884718450.107461199553-0.0134946335514-0.0935413366850.0108691950655-0.1739716324760.09750898861090.007118636015810.02607380145670.1231407767340.04256308030360.109295089215-19.9653822489.43983649721-13.2655016886
22.408590133740.28487434888-0.5363513221071.01680419453-0.07549424838162.391840146160.07102127357620.0776371931070.2177260495210.009769522504080.0149076872810.0817745002935-0.108424779981-0.0650490851961-0.03733999090350.0908725346539-0.001768334930870.01243458807250.0907152126259-0.0005142545297970.0811399562673-26.92208696522.45623780647-5.30919200107
31.711794117280.343309294056-0.3367834848670.9189481507060.234261637892.481594772560.0223015464627-0.220914946135-0.1115505388770.0631473854446-0.0297175812323-0.036658692030.100601388602-0.04508378962680.01299700235270.0871789401310.0009417307599220.0004605811687890.09341069656560.008953657077290.0482004909525-21.5792060649-4.966586489441.71315066648
42.29344993011-0.3420990680990.1570676825041.89526137304-0.05701215895152.424508833360.114885216622-0.4129746151290.05664246783110.102697492858-0.1087383153530.0540377971991-0.01918309224790.156022087214-0.02909210589450.0737618856544-0.0230372487862-0.005851562550640.150747041024-0.03425636707610.108664719391-6.225309723852.196745521610.94348378142
52.123401193880.122531191986-0.1848876049682.95014038503-0.4031331991481.38245242750.04144880664840.01200397302780.0448514061843-0.093790663264-0.0126548791894-0.240202269770.001329367703220.138913579007-0.0534852763610.06975410654187.59466241288E-50.01765463602530.114127251306-0.02314248693870.0803741120273-9.322344317291.82731921873-5.125860728
63.69587889259-0.4935657667650.7485306556064.444618859750.5928832127481.71164259537-0.0171418500749-0.0710394282396-0.1639393944270.0352947605362-0.04741384248660.190794351420.01208750666370.08580060236330.005603115203630.1269936213110.005402467485430.005513169965330.09105793761840.0450458519130.231864054171-35.1882973583-32.58813615253.49803753713
73.66365370001-2.252305482721.012363959423.973699742710.08397552790352.176343151520.2011417286540.489406782599-0.0437542843748-0.862276553772-0.2700440652760.461344851436-0.1349249336390.1129650525250.04035957299050.278468240.0162151360242-0.07288473404020.1648854839620.04642565819660.368281676703-41.0066956015-31.3048914703-4.4453250388
80.248147125211-0.8967810781-0.305020963343.09256789190.8588694505540.2118764521540.0308709942801-0.155073638146-0.540701164228-0.30178832351-0.08511519418890.613997828320.0134633178584-0.124819739203-0.002886509943050.149956638833-0.0197613479009-0.004676890558440.09248997027790.08289675267140.453390232343-45.7778143574-24.25606816543.47350018361
90.6780117591811.86217914395-0.5833872806485.42745639321-1.264755136741.17395751152-0.0447623684611-0.296626018653-0.499929543910.227582200992-0.07279041639340.78434011367-0.0394175036568-0.195628119417-0.04605104368360.123944899866-0.01428378633420.07004583230270.2024388282990.1070793089560.546492903242-51.2436768359-26.17175372379.20079254948
100.8894514007350.172383894819-0.4520380645424.30595112479-0.3600876559890.475085827832-0.0324800650293-0.543404818049-0.2688806241230.6750524579510.003950823361180.0751117546931-0.001802297657870.1152594550650.09194956107540.205359926558-0.02232794596370.005451194029870.2434579624430.09963402065360.199978709344-37.9745586318-16.555181862214.6534226055
112.787426410041.74053793243-1.21063852037.4958906987-0.7395006603721.16051050788-0.0556898081113-0.33026875536-0.231469591470.276778286066-0.006630082656710.2399854177510.08393685546110.1343406318660.02231562092590.134917058679-0.001068330507220.01472779544090.2386147193330.05460835755560.175760279909-44.4159841535-13.874791695112.4977641078
122.572045836780.179954810197-1.65142043362.840687781980.2962897855173.660927934960.0128479991878-0.408651411568-0.1716682818830.1788705251150.2590463312440.117255587307-0.2537170527460.213619865648-0.1008152969260.199269215245-0.00370538153360.05284899264710.2110126725870.1104020073210.19882290549-36.4164593403-22.339120677213.7441822308
133.9037882976-0.962195940199-3.060734917323.03427108740.8098915273875.825114020880.144161636124-0.9616422325390.3885847941650.2642380174770.187889065702-0.49902112598-0.6521792270750.826265139096-0.3380089126980.217758074754-0.0561863955395-0.04984335373870.550424703437-0.0004133219327340.28002759404-24.6582716595-20.741855988114.2098544901
143.234409664830.707922902397-2.566366112434.66788749043-0.6443205918034.398114090680.0265142013584-0.495502339101-0.2183934809280.1540895663740.0193869021405-0.08557935192070.1180844541590.687832607353-0.05219676626640.139023660249-0.00864881425319-0.02008316278720.2485126971840.06624196391860.23624086728-28.9948546436-27.44214856699.72596911983
151.96630910736-0.799182484614-1.721789910424.562694033330.2382732014194.53353593171-0.0408098562741-0.535549520111-0.2317955513470.4558897934860.314949757953-0.412314273472-0.06573738580750.6958881010750.0590745248820.1944923272360.00269640848309-0.05456749015540.4578009434510.1010927889030.217979339559-28.3992132284-24.234913067116.8456002605
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 34 )
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 122 )
3X-RAY DIFFRACTION3chain 'A' and (resid 123 through 155 )
4X-RAY DIFFRACTION4chain 'A' and (resid 156 through 174 )
5X-RAY DIFFRACTION5chain 'A' and (resid 175 through 206 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 26 )
7X-RAY DIFFRACTION7chain 'B' and (resid 27 through 57 )
8X-RAY DIFFRACTION8chain 'B' and (resid 58 through 85 )
9X-RAY DIFFRACTION9chain 'B' and (resid 86 through 101 )
10X-RAY DIFFRACTION10chain 'B' and (resid 102 through 122 )
11X-RAY DIFFRACTION11chain 'B' and (resid 123 through 142 )
12X-RAY DIFFRACTION12chain 'B' and (resid 143 through 155 )
13X-RAY DIFFRACTION13chain 'B' and (resid 156 through 174 )
14X-RAY DIFFRACTION14chain 'B' and (resid 175 through 190 )
15X-RAY DIFFRACTION15chain 'B' and (resid 191 through 206 )

+
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://pdbjlc1.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