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- PDB-7tsw: Crystal Structure Of Human NADH-Cytochrome B5 Reductase T117D Mutant -

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Basic information

Entry
Database: PDB / ID: 7tsw
TitleCrystal Structure Of Human NADH-Cytochrome B5 Reductase T117D Mutant
ComponentsNADH-cytochrome b5 reductase 3
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


nitric-oxide synthase complex / cytochrome-b5 reductase / Vitamin C (ascorbate) metabolism / cytochrome-b5 reductase activity, acting on NAD(P)H / Phase I - Functionalization of compounds / blood circulation / AMP binding / cholesterol biosynthetic process / hemoglobin complex / nitric oxide biosynthetic process ...nitric-oxide synthase complex / cytochrome-b5 reductase / Vitamin C (ascorbate) metabolism / cytochrome-b5 reductase activity, acting on NAD(P)H / Phase I - Functionalization of compounds / blood circulation / AMP binding / cholesterol biosynthetic process / hemoglobin complex / nitric oxide biosynthetic process / FAD binding / lipid droplet / mitochondrial membrane / ADP binding / NAD binding / azurophil granule lumen / mitochondrial outer membrane / Neutrophil degranulation / endoplasmic reticulum membrane / endoplasmic reticulum / mitochondrion / extracellular region / membrane / cytosol / cytoplasm
Similarity search - Function
NADH:cytochrome b5 reductase-like / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Flavoprotein pyridine nucleotide cytochrome reductase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NADH-cytochrome b5 reductase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsZheng, A. / Thibodeau, P.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122091 United States
CitationJournal: To be published
Title: Structure Of wild-type Human NADH-Cytochrome B5 Reductase and mutants
Authors: Zheng, A. / Thibodeau, P.H.
History
DepositionJan 31, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADH-cytochrome b5 reductase 3
B: NADH-cytochrome b5 reductase 3
C: NADH-cytochrome b5 reductase 3
D: NADH-cytochrome b5 reductase 3
E: NADH-cytochrome b5 reductase 3
F: NADH-cytochrome b5 reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,70912
Polymers186,9966
Non-polymers4,7136
Water5,765320
1
A: NADH-cytochrome b5 reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9522
Polymers31,1661
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NADH-cytochrome b5 reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9522
Polymers31,1661
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NADH-cytochrome b5 reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9522
Polymers31,1661
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NADH-cytochrome b5 reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9522
Polymers31,1661
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: NADH-cytochrome b5 reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9522
Polymers31,1661
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: NADH-cytochrome b5 reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9522
Polymers31,1661
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)162.562, 79.986, 172.358
Angle α, β, γ (deg.)90.000, 98.672, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
NADH-cytochrome b5 reductase 3


Mass: 31165.955 Da / Num. of mol.: 6 / Mutation: T117D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYB5R3, DIA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00387
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.19 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / Details: PEG 4K 10%, 0.1M Tris-HCl pH 8.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.4→46.03 Å / Num. obs: 80627 / % possible obs: 94 % / Redundancy: 7.71 % / Biso Wilson estimate: 51.6 Å2 / Rmerge(I) obs: 0.111 / Rrim(I) all: 0.12 / Net I/σ(I): 8.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 8.62 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 3 / Num. unique obs: 7363 / Rrim(I) all: 0.5 / % possible all: 86.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Cootmodel building
PHENIXphasing
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1umk

1umk


Resolution: 2.4→38.66 Å / SU ML: 0.3781 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.8546
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2641 1999 2.48 %
Rwork0.2266 78547 -
obs0.2276 80546 93.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.3 Å2
Refinement stepCycle: LAST / Resolution: 2.4→38.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12918 0 318 320 13556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007313621
X-RAY DIFFRACTIONf_angle_d0.995718551
X-RAY DIFFRACTIONf_chiral_restr0.05841994
X-RAY DIFFRACTIONf_plane_restr0.00842371
X-RAY DIFFRACTIONf_dihedral_angle_d22.82245125
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.37921300.32045122X-RAY DIFFRACTION86.5
2.46-2.530.3441330.30275208X-RAY DIFFRACTION87.44
2.53-2.60.36341320.30995205X-RAY DIFFRACTION87.64
2.6-2.680.37071340.30835271X-RAY DIFFRACTION88.91
2.68-2.780.36231370.31285342X-RAY DIFFRACTION89.94
2.78-2.890.36851380.30595426X-RAY DIFFRACTION91.26
2.89-3.020.35631420.30225580X-RAY DIFFRACTION93.25
3.02-3.180.31971430.30185676X-RAY DIFFRACTION95.74
3.18-3.380.32921470.2765802X-RAY DIFFRACTION96.86
3.38-3.640.27961510.23315876X-RAY DIFFRACTION98.43
3.64-4.010.24081500.21115932X-RAY DIFFRACTION99.35
4.01-4.590.22771520.17615976X-RAY DIFFRACTION99.64
4.59-5.780.20041540.17846033X-RAY DIFFRACTION99.95
5.78-38.660.20331560.17996098X-RAY DIFFRACTION99.14
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)
12.955710593212.03539636058-0.9586879963984.403246989881.346050951851.71762621924-0.5298202223111.850340584660.339091201209-1.177926435230.7566980455940.0470402498408-0.2788002017230.0363417121642-0.2028058533180.76131296834-0.312815193225-0.1115574640841.501615772880.1600993691330.559801759448-69.7789650946-60.280971796646.3200738657
27.256802266273.182577641150.890253982764.232544096420.6451000884322.5290860552-0.0232012203436-0.974513238981-0.281968242599-0.170386173211-0.35262126943-0.0936037307845-0.03023025227480.01388831513640.3757293813460.3040767794890.07601174384940.0306033639310.4322615308690.04376779077390.482289318585-7.2924676567-32.267806023620.6582292363
32.49999132081-0.090290605096-0.2000947776264.221212360971.685167651973.520508537140.13294906855-1.114633540910.1709951034430.784279267083-0.4328361542130.735667498588-0.20258098832-0.3120370842960.2600483119730.591830518371-0.1642439053770.1414803946451.04976434292-0.1520683519910.72166877119-15.0585711324-23.9186711339.2397274682
42.78599023444-0.569966212671-0.3957069792074.954199282220.01884010313992.82093112299-0.003371426331560.1808302645350.24483747896-0.33070643534-0.00222955796328-0.709963615029-0.02400892209430.2221171559660.01423570254620.3564712229120.01916934573770.05939138632990.2513650872270.02734227842270.409692952512-29.018231733-18.1196385831-12.2143030822
53.2113914279-1.199132144340.02484122246475.037645639050.2439912270512.59418337435-0.03695859210150.08368089810760.211476598647-0.2369094317820.0369947535950.0304844130485-0.205766245647-0.1928590405160.03105766071220.4108527004910.02608027709770.009769691542080.2782585805650.00722115619530.317603155695-39.5214098629-13.9352303145-10.7175750785
63.7578024494-0.568595836435-0.06074098985113.21727165918-0.5651679869161.96013178006-0.0239701612425-0.002463167064080.244175040250.3066443944120.0553473797305-0.574986709697-0.09071483958380.297486237801-0.01871571380930.363833677186-0.0050596530052-0.07921857176410.295712810666-0.05164559354590.380280396748-28.0360788954-22.52949009797.72677882234
73.95911110521-0.544886640159-0.1149704418024.58190678407-0.04768376826561.84416622913-0.0708162531245-0.206995614079-0.05740483379390.2369453883030.1405905662280.1359639855020.137742105134-0.122442772284-0.0586298054990.3838122266390.00932769902001-0.0353474064150.2758677055240.009754486323820.284677121999-41.5670754329-27.059851917710.6942726708
83.84315653102-0.6422208726171.648445707075.009137928680.07106665840074.387634763620.2388016464840.108817512995-0.142231349261-0.656524023379-0.1690843279470.5766485706640.200027326537-0.566758890719-0.06356160144110.5917935119390.048377786876-0.05631644554770.453358139593-0.05596821025780.455440909222-72.9292234277-28.992204116670.8911781814
92.355591644840.2887141743980.3408179507884.13657228243-0.2033896779892.232993771190.0533930496402-0.3422275482-0.1037218088750.583719005418-0.09286481349430.2677100033360.0317795607841-0.1559666995720.04694256902030.4326602396810.01715630393290.05366979094510.387462396301-0.04570683421340.382939245243-66.5161348827-36.168657422390.3335328358
103.676229802431.085778513611.483549343871.861700689070.9017045212753.33494636846-0.2678387874421.116852895080.216780032811-0.3660074760520.196294197818-0.05084396799-0.01810438692910.3167209573780.08380048436490.408160846643-0.06493571472740.06329323290060.6419445056640.09199510844430.370251261696-38.6037764652-43.61758920356.7117381886
113.27145964121-0.02300021252110.07160431390753.898148131610.4307782751772.12535734884-0.1257302729020.271551477312-0.1007930069480.01271040470930.0573250481126-0.3353582143320.1425674111090.4345040489770.08538969361210.3750912763590.03836154482330.03711290064320.4999063654990.03887695133580.359753754625-24.0504152177-49.259628532470.692154495
124.40841047530.918523454146-0.717641005064.10111725869-2.802313776126.609458365630.575046097986-1.34164217031-0.3165681896291.19653813035-0.51711551756-0.0889345885511-0.06305058504320.664848144628-0.06589289676450.758787446386-0.0819092882493-0.01909756568340.7457210708050.03621318107150.406319658366-48.6985118136-10.426871987639.2100886494
134.969602236011.67208177597-1.233230312494.94396940236-1.91319636673.783716313480.2323704328840.02539409540580.1833828315650.01835680936380.2360758961860.815542689047-0.0604381873852-0.313581858581-0.4355875202050.3566823278360.05455998105310.033287003370.2842707922740.0498001571620.435472210348-59.6536513674-4.0838641356820.8872507102
143.486484187061.78104376215-0.5535627361893.59688277401-0.5394234343694.16932517436-0.1599078697880.499784420337-0.24738531003-0.3517916801890.165730156935-0.02244550864440.00314377253203-0.3561418171760.008908428739250.385498395111-0.03681844525050.01632458847290.435908510034-0.067844596270.352232899495-71.5661278921-73.188579762868.3211771072
156.78061101880.14073249137-2.161014206833.846487016750.2401442161493.0551345091-0.6857065071771.31354962833-0.813008721931-0.7161623432070.46177908904-0.50830284830.328805403390.06408322794180.1745874044310.537583724041-0.1526690693210.09346759891180.669774132957-0.2046141884830.456134517193-60.6551555491-67.19630760855.7586780873
164.328624126820.87512966849-0.7000680993455.31553996962-1.190689794042.08969112408-0.03892253893790.4991816154820.2245535179160.2136114203220.1401029950480.0449045555775-0.0219664450005-0.000972155905523-0.07497215526510.412334505067-0.07907680510610.01116967518720.516279719662-0.0506744531150.30817229852-59.0578028044-54.445203894459.0646506731
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'E' and (resid 255 through 301 )EI255 - 301217 - 263
22chain 'F' and (resid 31 through 138 )FK31 - 1381 - 108
33chain 'F' and (resid 139 through 301 )FK139 - 301109 - 271
44chain 'A' and (resid 31 through 78 )AA31 - 781 - 48
55chain 'A' and (resid 79 through 143 )AA79 - 14349 - 113
66chain 'A' and (resid 144 through 210 )AA144 - 210114 - 180
77chain 'A' and (resid 211 through 301 )AA211 - 301181 - 271
88chain 'B' and (resid 31 through 138 )BC31 - 1381 - 108
99chain 'B' and (resid 139 through 301 )BC139 - 301109 - 271
1010chain 'C' and (resid 31 through 173 )CE31 - 1731 - 143
1111chain 'C' and (resid 174 through 301 )CE174 - 301144 - 271
1212chain 'D' and (resid 32 through 153 )DG32 - 1531 - 122
1313chain 'D' and (resid 154 through 301 )DG154 - 301123 - 270
1414chain 'E' and (resid 31 through 173 )EI31 - 1731 - 135
1515chain 'E' and (resid 174 through 210 )EI174 - 210136 - 172
1616chain 'E' and (resid 211 through 254 )EI211 - 254173 - 216

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