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- PDB-7n7s: Crystal Structure of Hydroxymethylglutaryl-CoA reductase from Eli... -

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Basic information

Entry
Database: PDB / ID: 7n7s
TitleCrystal Structure of Hydroxymethylglutaryl-CoA reductase from Elizabethkingia anophelis NUHP1
ComponentsHydroxymethylglutaryl-CoA reductase
KeywordsOXIDOREDUCTASE / SSGCID / hydroxymethylglutaryl-CoA reductase / HGM-CoA reductase / Elizabethkingia anophelis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


hydroxymethylglutaryl-CoA reductase (NADPH) activity / coenzyme A metabolic process
Similarity search - Function
Hydroxymethylglutaryl-CoA reductase, bacterial-type / Hydroxymethylglutaryl-coenzyme A reductases signature 1. / Hydroxymethylglutaryl-CoA reductase, class I/II / Hydroxymethylglutaryl-CoA reductase, class I/II, NAD/NADP-binding domain superfamily / Hydroxymethylglutaryl-CoA reductase, class I/II, substrate-binding domain superfamily / Hydroxymethylglutaryl-CoA reductase, class I/II, catalytic domain superfamily / Hydroxymethylglutaryl-CoA reductase, class I/II, conserved site / Hydroxymethylglutaryl-coenzyme A reductase / Hydroxymethylglutaryl-coenzyme A reductases family profile.
Similarity search - Domain/homology
CITRIC ACID / Hydroxymethylglutaryl-CoA reductase
Similarity search - Component
Biological speciesElizabethkingia anophelis NUHP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be published
Title: Crystal Structure of Hydroxymethylglutaryl-CoA reductase from Elizabethkingia anophelis NUHP1
Authors: Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJun 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hydroxymethylglutaryl-CoA reductase
B: Hydroxymethylglutaryl-CoA reductase
C: Hydroxymethylglutaryl-CoA reductase
D: Hydroxymethylglutaryl-CoA reductase
E: Hydroxymethylglutaryl-CoA reductase
F: Hydroxymethylglutaryl-CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)310,69657
Polymers305,2546
Non-polymers5,44251
Water22,0141222
1
A: Hydroxymethylglutaryl-CoA reductase
B: Hydroxymethylglutaryl-CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,67320
Polymers101,7512
Non-polymers1,92118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14320 Å2
ΔGint-274 kcal/mol
Surface area32380 Å2
MethodPISA
2
C: Hydroxymethylglutaryl-CoA reductase
E: Hydroxymethylglutaryl-CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,54319
Polymers101,7512
Non-polymers1,79117
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13230 Å2
ΔGint-245 kcal/mol
Surface area28800 Å2
MethodPISA
3
D: Hydroxymethylglutaryl-CoA reductase
F: Hydroxymethylglutaryl-CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,48018
Polymers101,7512
Non-polymers1,72916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13170 Å2
ΔGint-237 kcal/mol
Surface area28920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.850, 206.670, 90.400
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

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Components

#1: Protein
Hydroxymethylglutaryl-CoA reductase


Mass: 50875.684 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia anophelis NUHP1 (bacteria)
Gene: BD94_0681 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A077EA44
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1222 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.82 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Anatrace / Calibre Top96 screen, condition F1: 200 mM potassium sodium tartrate, 100 mM sodium citrate / citric acid pH 5.6, 2 M ammonium sulphate: ElanA.19063.a.B1.PS38245 at 23.3 mg/ml: ...Details: Anatrace / Calibre Top96 screen, condition F1: 200 mM potassium sodium tartrate, 100 mM sodium citrate / citric acid pH 5.6, 2 M ammonium sulphate: ElanA.19063.a.B1.PS38245 at 23.3 mg/ml: tray 290979 F1: cryo: 25% EG: puck ywm0-9.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 7, 2019 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 135029 / % possible obs: 100 % / Redundancy: 8.357 % / Biso Wilson estimate: 45.851 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.085 / Χ2: 1.003 / Net I/σ(I): 19.24
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.4-2.468.4530.563.9298700.8990.596100
2.46-2.538.4490.4464.8896390.9330.475100
2.53-2.68.4370.3865.6293840.9490.411100
2.6-2.688.4350.3426.3791300.9590.365100
2.68-2.778.4240.268.2288290.9760.277100
2.77-2.878.4220.2149.9485390.9840.228100
2.87-2.988.3990.17711.7983000.9880.189100
2.98-3.18.4010.14414.1579420.9920.153100
3.1-3.248.3680.10918.0576610.9950.116100
3.24-3.398.3810.08622.1672940.9960.092100
3.39-3.588.370.07225.8669650.9980.077100
3.58-3.798.3670.06129.4466390.9980.06599.9
3.79-4.068.3550.05333.3861940.9980.056100
4.06-4.388.3460.04537.958120.9990.048100
4.38-4.88.3120.04239.9153770.9990.045100
4.8-5.378.2810.04239.7148720.9990.045100
5.37-6.28.2230.04537.9843140.9990.048100
6.2-7.598.1170.04239.8937070.9990.045100
7.59-10.737.910.03646.7829010.9990.039100
10.73-507.0810.03645.5316600.9990.03997.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19 4224refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 5wpjA as per Morda

Resolution: 2.4→49.26 Å / SU ML: 0.2048 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.2656
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1876 1956 1.45 %0
Rwork0.1532 133056 --
obs0.1537 135012 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.48 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18621 0 302 1222 20145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005219485
X-RAY DIFFRACTIONf_angle_d0.701226461
X-RAY DIFFRACTIONf_chiral_restr0.04662945
X-RAY DIFFRACTIONf_plane_restr0.00453398
X-RAY DIFFRACTIONf_dihedral_angle_d14.28067021
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.21261220.18799418X-RAY DIFFRACTION99.98
2.46-2.530.22451560.17889399X-RAY DIFFRACTION100
2.53-2.60.20361330.18249420X-RAY DIFFRACTION99.99
2.6-2.680.25031310.18679410X-RAY DIFFRACTION100
2.68-2.780.21791410.17379388X-RAY DIFFRACTION100
2.78-2.890.20941230.17439475X-RAY DIFFRACTION99.98
2.89-3.020.23361390.18349429X-RAY DIFFRACTION100
3.02-3.180.22591370.18539466X-RAY DIFFRACTION99.98
3.18-3.380.19341550.16529462X-RAY DIFFRACTION99.99
3.38-3.640.20251540.15739478X-RAY DIFFRACTION99.98
3.64-4.010.17911500.14059504X-RAY DIFFRACTION99.96
4.01-4.590.12891560.1169561X-RAY DIFFRACTION99.98
4.59-5.780.16591150.12459683X-RAY DIFFRACTION100
5.78-49.260.17841440.15129963X-RAY DIFFRACTION99.74
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.479301126270.287466872917-0.09539705013670.615108214132-0.1168310001481.14522355161-0.006308256287390.03496398946550.2457327718980.117467988420.0167415942798-0.151239048209-0.1951527693050.2195177863160.0008796306579710.377019771031-0.024069588812-0.1346096793060.401605761847-0.01894011848130.443461324196105.46814290972.246351286448.2525842726
22.641971604140.7281926492460.482732116923.805219847661.342021284422.16452891123-0.100084227360.318291393299-0.0719575658817-0.05499848424550.197024078077-0.281440122938-0.05748611766860.434918266801-0.09418211680280.210411759337-0.0177942554264-0.04498058580620.371169671048-0.01427707505540.2643446752695.275168884842.858327023227.3867148992
33.51989180303-0.0404968980258-0.1027395762061.111167377060.1084175244031.51176105524-0.0182114615143-0.2307654413660.1868042738930.0715021683280.02538128267330.122338096347-0.033205723213-0.225373575388-0.02366002377060.282461261706-0.00803431382852-0.104056684930.320059832637-0.02517988309970.30110513980984.526075294664.268785117852.4972295816
40.700111566855-0.2097083453760.2096185884790.765631545608-0.4201616942811.18792911812-0.0554052671059-0.0358778454020.10868288465-0.03807283416410.1027139546920.0267156431681-0.0596115627694-0.239736646141-0.0478282003970.356083855120.0572900510738-0.0367834030940.351908129450.0902282187160.39859868293135.137935755291.222570673210.4842161846
53.54100386208-0.967553311593-0.04844895786851.416590086010.6870583253241.496380604870.05111740970980.2020796385650.525868763048-0.0619836901978-0.10277376002-0.213113098804-0.2679012391780.1223325471940.04351946551460.433158127484-0.054145391128-0.1109943967310.3607665807350.1329471773010.49969506842571.687653096891.328166052417.4536390766
62.61604454307-0.498134024491-1.311161920251.00287717662-0.5430353668112.55120468445-0.1238572935620.0684490893460.3202466388590.03564662178460.150705492865-0.03032131335450.164560400687-0.0626552504305-0.03191311824660.3703381723290.0104283739784-0.1170988205790.2971045409760.02132050261280.3414905920258.34570256883.019168131324.8489235172
71.78810328718-0.9359944405120.2999654371432.77948264166-0.4300778653311.61751960643-0.139590792318-0.306966456715-0.06392567727650.3473816677370.2010400527020.0854302615013-0.0054901673836-0.156989101157-0.04675823252830.2979000540860.0417799331349-0.06908269891760.3418389207960.07273585055140.29722990532842.604546702981.126822344328.1899662139
80.999188400377-0.1854612050780.5893805935160.233964361619-0.02960880942640.597959626889-0.0953723465566-0.1609286872370.2678166147620.1195489092670.040950921293-0.105762726284-0.166725328086-0.009019654036730.04935119648480.408920211283-0.0203891797761-0.1117574757580.351449679495-0.01741824037980.43668609172186.88181783780.73760565446.0882798061
92.418402096140.3797936502530.7733208348211.793880632820.4428820773852.00470598012-0.05841238557370.366431369310.0843210759466-0.1517751063890.0592228701501-0.0479487615109-0.01890638152670.0993891437068-0.009269368166930.301079778728-0.0305413321417-0.1152914773690.3993302476370.0540926716070.36068008620495.80430897771.071129066127.4186024
101.942891904120.819543155557-1.012564935961.54833090013-0.3448166103761.80990698118-0.1201525015210.091620165906-0.1156905606880.0685330719470.09614033051290.1577947436920.262069493257-0.1877134311430.03246848010920.2502570948060.02323565822-0.02976204334670.190839492503-0.03830590298540.2695943471556.510508854212.777279013721.8329142322
111.919640208590.1505404492650.3601293451113.375940504061.875499067773.000726305140.0137597348772-0.174320556094-0.09867103080060.640274223917-0.00342440262202-0.1186320399480.3522219160940.100581412445-0.02727249289260.356121641498-0.0119194141835-0.04395489963980.2974991227140.03138442006090.21334276640276.405438543433.742697908646.4223139537
121.109171607060.439147178765-0.1630373046573.10923808351-0.1134363218731.29899675669-0.04313966004860.171471892860.0623856863378-0.245080005010.09892953021230.00457313390291-0.03784750907590.0773210442877-0.06518351509150.216164289866-0.0143816516871-0.02352518106460.246392125084-0.0390129020580.23136434579969.737198231829.773010220812.3868164412
130.5044477245350.0172716450612-0.09780054481751.03800296843-0.1007153924160.68995266786-0.04222908369620.11137129906-0.0785820802995-0.1153527676320.06798184020930.1121404873190.0676432354543-0.0259890789365-0.04093488104360.227453360523-0.0405751114471-0.03482195783720.257629809083-0.03112156737980.27633771924152.839909272922.126924624315.1922328136
141.89255706870.732894213899-0.3370873385333.33046176802-0.4821744323971.73392346918-0.1030863089220.262629829580.0187352421102-0.7343301232480.1354246304290.0583183327170.00216166982319-0.0374795343629-0.05617725748570.371757751867-0.00898491695832-0.03909906676890.2705475177770.002277071272730.23426019686750.043453095543.53343064772.7654681823
152.184274875470.5677765464950.0466434895113.097484451630.005623986540834.368373616690.153613484407-0.6370553745680.03960132539771.03706962497-0.193283244890.1608290421430.5111412020330.2541625340910.009198912872090.60861991250.03198418900320.09060151760880.403662582718-0.01292194607050.35164033274245.915626403732.377941995945.5275869954
161.675058320620.471482119672-0.1299469033512.626607388390.2542717537531.433742894740.05619314855-0.1823574235160.16422357320.2477327442680.03341503656840.134437707591-0.0816647542633-0.0668289677366-0.08532321731810.2273663011810.02698522911940.02628145611590.211636527961-0.007172587491820.23875448131852.399780492831.22701393631.2398781312
171.204478529451.01633797690.2372813112872.137494656081.741378052472.061697611290.190460934283-0.599668944998-0.2249383256830.8248267764010.121800372178-0.003121390763770.157813399698-0.132731921662-0.240326531050.515801636360.02505703017850.006484217174950.370360913356-0.01675694384780.27020690848657.029725281128.746451535147.3045242536
185.26599774117-0.7018932862390.4978181461082.401820752692.248445633548.35862349902-0.09161346142690.543503822635-0.66663761659-1.29005221842-0.2457795444160.1079558559650.813038373139-0.3060725555730.3289064397541.19044222606-0.08356356521660.01148710510730.652691638385-0.09288667284910.4747949266475.479856331625.688621956872.070824643
190.121268109202-0.150975587864-0.07966325840991.3375561094-0.4240379115190.358683065941-0.07368568758150.0205733617120.03864975865740.01168398544030.06822454886920.167212789293-0.0578339258302-0.154590889530.005858595483020.2740322327440.0299037156995-0.05365933575240.354066360990.05957165295620.35098138989133.521757986671.743777339317.2943067653
203.29184384169-1.054216788390.4720657344412.1581510499-0.5644886824821.664055426940.06370845090350.1773893498830.156557583946-0.207476632687-0.114218382276-0.2938274057510.07793615092710.1974360051660.02427838364110.3326045857750.0163522540122-0.02639508442240.2457125614670.09518487263670.36184857206751.275779468976.45888197683.69688400917
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'D' and (resid 2 through 114 )DD2 - 1141 - 113
22chain 'D' and (resid 115 through 235 )DD115 - 235114 - 234
33chain 'D' and (resid 236 through 390 )DD236 - 390235 - 389
44chain 'E' and (resid 2 through 114 )EE2 - 1141 - 113
55chain 'E' and (resid 115 through 210 )EE115 - 210114 - 209
66chain 'E' and (resid 211 through 256 )EE211 - 256210 - 255
77chain 'E' and (resid 257 through 390 )EE257 - 390256 - 389
88chain 'F' and (resid 2 through 235 )FF2 - 2351 - 234
99chain 'F' and (resid 236 through 390 )FF236 - 390235 - 389
1010chain 'A' and (resid -3 through 114 )AA-3 - 1141 - 118
1111chain 'A' and (resid 115 through 235 )AA115 - 235119 - 239
1212chain 'A' and (resid 236 through 390 )AA236 - 390240 - 394
1313chain 'B' and (resid 2 through 156 )BL2 - 1561 - 155
1414chain 'B' and (resid 157 through 235 )BL157 - 235156 - 234
1515chain 'B' and (resid 236 through 256 )BL236 - 256235 - 255
1616chain 'B' and (resid 257 through 364 )BL257 - 364256 - 363
1717chain 'B' and (resid 365 through 407 )BL365 - 407364 - 406
1818chain 'B' and (resid 408 through 442 )BL408 - 442407 - 441
1919chain 'C' and (resid 2 through 235 )CU2 - 2351 - 234
2020chain 'C' and (resid 236 through 390 )CU236 - 390235 - 389

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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

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