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- PDB-6vjr: Oxygen tolerant Archeal 4hydroxybutyrylCoA dehydratase (4HBD) fro... -

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Basic information

Entry
Database: PDB / ID: 6vjr
TitleOxygen tolerant Archeal 4hydroxybutyrylCoA dehydratase (4HBD) from N. maritimus
ComponentsVinylacetyl-CoA Delta-isomerase
KeywordsPROTEIN BINDING / oxygen tolerance / iron-sulfur cluster / ammonia-oxidizing archaea / bioenergy / C-cycling
Function / homology
Function and homology information


vinylacetyl-CoA Delta-isomerase / vinylacetyl-CoA delta-isomerase activity / oxidoreductase activity, acting on the CH-CH group of donors / 4 iron, 4 sulfur cluster binding / nucleotide binding / metal ion binding
Similarity search - Function
HpaB/PvcC/4-BUDH / HpaB/PvcC/4-BUDH N-terminal / HpaB/PvcC/4-BUDH C-terminal / 4-hydroxyphenylacetate 3-hydroxylase C terminal / 4-hydroxyphenylacetate 3-hydroxylase N terminal / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / : / PHOSPHATE ION / IRON/SULFUR CLUSTER / Vinylacetyl-CoA Delta-isomerase
Similarity search - Component
Biological speciesNitrosopumilus maritimus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsDeMirci, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1231306 United States
CitationJournal: To Be Published
Title: Structural adaptation of oxygen tolerance in a key archaeal carbon fixation enzyme
Authors: Demirci, H. / Wakatsuki, S.
History
DepositionJan 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: Vinylacetyl-CoA Delta-isomerase
B: Vinylacetyl-CoA Delta-isomerase
C: Vinylacetyl-CoA Delta-isomerase
D: Vinylacetyl-CoA Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,99521
Polymers224,7434
Non-polymers5,25117
Water30,6261700
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35730 Å2
ΔGint-371 kcal/mol
Surface area57580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.530, 72.954, 180.517
Angle α, β, γ (deg.)90.000, 98.380, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Vinylacetyl-CoA Delta-isomerase


Mass: 56185.863 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosopumilus maritimus (strain SCM1) (archaea)
Strain: SCM1 / Gene: Nmar_0207 / Production host: Escherichia coli (E. coli)
References: UniProt: A9A1Y2, vinylacetyl-CoA Delta-isomerase

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Non-polymers , 6 types, 1717 molecules

#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1700 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 294 K / Method: microbatch / pH: 8
Details: 0.1 M Li2SO4, 0.1 M Tris, pH 8 25 % v/v Jeffamine ED-2003

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.55→40 Å / Num. obs: 319062 / % possible obs: 97.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.06 / Rrim(I) all: 0.159 / Χ2: 1.247 / Net I/σ(I): 7.4 / Num. measured all: 2104789
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.55-1.615.90.693316300.8940.2930.7540.60497.4
1.61-1.676.50.569315870.8790.2350.6170.68897.4
1.67-1.756.60.471317690.9460.1930.510.81897.8
1.75-1.846.40.345318870.9580.1440.3741.02598.1
1.84-1.956.40.254312550.970.1060.2751.38896.2
1.95-2.170.187321800.9850.0750.2011.35298.9
2.1-2.326.90.202322930.9870.0850.221.66699.1
2.32-2.656.40.143316020.9860.0590.1551.58196.7
2.65-3.3470.136323680.9770.0550.1461.72198.9
3.34-406.80.106324910.9920.0430.1151.46297.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphenix-dev-3318refinement
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U8V

1u8v


Resolution: 1.55→34.858 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.09
RfactorNum. reflection% reflection
Rfree0.1746 1998 0.63 %
Rwork0.1579 --
obs0.158 318601 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 229.52 Å2 / Biso mean: 23.0608 Å2 / Biso min: 7.14 Å2
Refinement stepCycle: final / Resolution: 1.55→34.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15706 0 273 1734 17713
Biso mean--38.45 35.97 -
Num. residues----2002
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.55-1.58880.22941420.21152239597
1.5888-1.63170.20561400.19852242198
1.6317-1.67970.2241430.1932242797
1.6797-1.73390.20931410.18742250998
1.7339-1.79590.2181420.19332257198
1.7959-1.86780.22061410.18612213296
1.8678-1.95280.21671410.18182245598
1.9528-2.05580.19121450.17112281899
2.0558-2.18450.20481430.16362284199
2.1845-2.35320.16281450.15732290899
2.3532-2.58990.18281430.15892273498
2.5899-2.96450.18651400.15472223196
2.9645-3.73430.13931470.136423206100
3.7343-34.850.13971450.13532295597
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)
15.784-1.91242.53781.5204-0.5722.7605-0.1028-0.06140.21610.1089-0.0024-0.0225-0.1796-0.13260.06340.1330.00910.02910.11320.01170.109713.303-9.00774.952
22.31252.1797-0.02363.07850.53271.50580.0218-0.03820.07460.0216-0.0150.3057-0.0715-0.33770.00780.09450.0388-0.01310.17460.03280.1424.501-9.93556.062
31.2435-0.31710.21130.90710.07620.9384-0.0063-0.0656-0.15910.02450.02580.12590.1497-0.2148-0.01470.1539-0.04870.00520.15310.04250.14389.536-29.81262.548
42.2611-0.5379-0.05874.57380.99471.29320.0547-0.0321-0.1829-0.1064-0.05750.05890.0996-0.1910.00580.1273-0.0181-0.00540.11180.0460.100213.632-30.96867.528
50.31270.25320.00350.602-0.05390.51650.0048-0.0496-0.00560.01960.01130.0357-0.0271-0.0944-0.01990.11870.0223-0.00360.10740.01270.127921.016-12.02462.046
60.67840.36440.2360.63870.31920.74190.0007-0.03930.04040.02410.02540.0002-0.0889-0.0553-0.01820.14170.0229-0.00680.09260.01520.112126.924-3.95660.262
71.26860.268-0.12780.6209-0.32591.6685-0.03590.0738-0.1099-0.02450.05350.19950.2882-0.49160.03090.1645-0.0469-0.0210.1707-0.0010.192219.44-26.13631.82
85.10561.97841.08721.8901-0.27990.9334-0.0940.06990.1691-0.15660.01520.0333-0.1140.15810.03520.13770.00540.03070.1314-0.02130.103762.025-11.53614.528
90.8788-1.14320.18962.967-0.21021.04910.02610.0351-0.0337-0.01880.0129-0.18990.03760.3133-0.03020.1003-0.0027-0.00350.24-0.04010.157371.598-19.37132.384
101.79330.2321-0.31741.3622-0.241.0315-0.04080.0341-0.36480.00550.0144-0.05820.29610.14510.04880.22950.0533-0.01440.1337-0.04380.181556.439-38.31324.867
111.0675-0.92550.36762.4404-0.53990.92710.03940.0829-0.063-0.0139-0.01860.01650.02990.1212-0.02250.1592-0.00160.00430.1402-0.04040.123857.291-24.09119.815
120.6135-0.5469-0.07021.07410.08690.5603-0.00960.0203-0.01840.00780.0245-0.0384-0.00850.1154-0.01990.1012-0.0214-0.01410.1099-0.01790.100855.52-13.80233.288
130.6335-0.29740.21370.6196-0.26150.7156-0.00090.06280.0424-0.05670.0155-0.0028-0.09890.0747-0.00960.133-0.024-0.00110.0809-0.01340.085748.476-5.01228.512
141.19640.0152-0.96130.30050.0993.9013-0.0679-0.143-0.17530.04670.0249-0.15160.40420.31180.07080.16440.0445-0.02460.12520.01440.187253.026-25.92559.198
153.0873-3.22711.74514.2248-4.10717.10570.23240.9710.3565-0.6813-0.2245-1.99180.25991.22820.02410.3538-0.0450.08640.6922-0.15070.603872.995-18.2357.271
161.3327-0.1062-0.21831.0551-0.17120.7901-0.0452-0.1606-0.110.08250.0165-0.1068-0.0070.32220.00270.1564-0.0121-0.06170.2328-0.03750.127760.33-6.41975.764
170.76440.7494-0.09462.35640.36770.8060.0272-0.11120.15350.05740.0577-0.066-0.1630.2886-0.08310.1476-0.0411-0.02720.228-0.05590.152765.4672.84365.593
180.84540.192-0.02461.0815-0.00260.78470.0245-0.08320.14030.0155-0.0148-0.0533-0.19960.14150.00070.2108-0.025-0.01160.1386-0.04970.134649.3589.93972.485
190.5110.4274-0.04661.01110.18820.543-0.005-0.07230.05-0.02470.0254-0.0554-0.11730.1221-0.02770.1237-0.0041-0.02250.1041-0.01720.106651.451-4.64260.717
200.44420.1309-0.14490.4142-0.09460.61530.0124-0.05780.00340.04470.02-0.0096-0.03720.0695-0.0250.12930.0086-0.0230.0973-0.01270.10544.837-10.27760.023
210.87370.32141.46661.440.26764.201-0.12260.11420.3110.0391-0.0028-0.2365-0.560.52230.1740.2093-0.0890.0230.2128-0.00690.244361.626.63132.643
221.89120.2665-0.43530.97550.21221.0586-0.07980.2131-0.1021-0.10590.01710.10390.0173-0.32050.02050.19420.001-0.07010.24160.03330.140115.464-9.00813.26
233.3929-3.01070.59754.1458-0.14921.8234-0.07990.0815-0.0769-0.09420.09170.2466-0.0552-0.3226-0.01110.1007-0.0252-0.03360.1540.03290.09712.609-9.526.936
241.3344-1.1215-0.70494.92191.44791.5435-0.00960.0780.1518-0.03620.00950.1513-0.2002-0.35150.01190.19660.0686-0.02360.25230.07870.16668.6586.80220.747
250.7683-0.1509-0.07481.03560.05210.82220.01980.09960.1432-0.0502-0.01390.0674-0.2414-0.12520.00320.2370.0193-0.02670.14890.04820.129726.1647.75115.515
260.6352-0.4157-0.01990.9389-0.14610.6309-0.00490.08750.0232-0.00790.02590.0954-0.1128-0.1306-0.03770.131-0.0005-0.02870.10390.01280.092823.863-5.75728.287
270.8383-0.3898-0.29290.65570.22570.61520.01430.0757-0.0191-0.06160.0185-0.0114-0.0033-0.0611-0.02580.1409-0.0133-0.02470.09320.01060.091431.6-14.46826.666
280.7552-0.0502-0.21910.480.18012.85950.04090.05090.1603-0.04530.01470.1581-0.3272-0.3537-0.05090.20280.0655-0.00880.140.01650.202617.187.6552.46
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 28:58 )A28 - 58
2X-RAY DIFFRACTION2( CHAIN A AND RESID 59:102 )A59 - 102
3X-RAY DIFFRACTION3( CHAIN A AND RESID 103:183 )A103 - 183
4X-RAY DIFFRACTION4( CHAIN A AND RESID 184:231 )A184 - 231
5X-RAY DIFFRACTION5( CHAIN A AND RESID 232:340 )A232 - 340
6X-RAY DIFFRACTION6( CHAIN A AND RESID 341:458 )A341 - 458
7X-RAY DIFFRACTION7( CHAIN A AND RESID 459:508 )A459 - 508
8X-RAY DIFFRACTION8( CHAIN B AND RESID 28:58 )B28 - 58
9X-RAY DIFFRACTION9( CHAIN B AND RESID 59:147 )B59 - 147
10X-RAY DIFFRACTION10( CHAIN B AND RESID 148:183 )B148 - 183
11X-RAY DIFFRACTION11( CHAIN B AND RESID 184:264 )B184 - 264
12X-RAY DIFFRACTION12( CHAIN B AND RESID 265:340 )B265 - 340
13X-RAY DIFFRACTION13( CHAIN B AND RESID 341:458 )B341 - 458
14X-RAY DIFFRACTION14( CHAIN B AND RESID 459:501 )B459 - 501
15X-RAY DIFFRACTION15( CHAIN B AND RESID 502:507 )B502 - 507
16X-RAY DIFFRACTION16( CHAIN C AND RESID 29:77 )C29 - 77
17X-RAY DIFFRACTION17( CHAIN C AND RESID 78:147 )C78 - 147
18X-RAY DIFFRACTION18( CHAIN C AND RESID 148:264 )C148 - 264
19X-RAY DIFFRACTION19( CHAIN C AND RESID 265:340 )C265 - 340
20X-RAY DIFFRACTION20( CHAIN C AND RESID 341:476 )C341 - 476
21X-RAY DIFFRACTION21( CHAIN C AND RESID 477:506 )C477 - 506
22X-RAY DIFFRACTION22( CHAIN D AND RESID 29:76 )D29 - 76
23X-RAY DIFFRACTION23( CHAIN D AND RESID 77:102 )D77 - 102
24X-RAY DIFFRACTION24( CHAIN D AND RESID 103:147 )D103 - 147
25X-RAY DIFFRACTION25( CHAIN D AND RESID 148:264 )D148 - 264
26X-RAY DIFFRACTION26( CHAIN D AND RESID 265:340 )D265 - 340
27X-RAY DIFFRACTION27( CHAIN D AND RESID 341:458 )D341 - 458
28X-RAY DIFFRACTION28( CHAIN D AND RESID 459:506 )D459 - 506

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