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- PDB-7u6h: HalD with ornithine and alpha-ketoglutarate -

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Basic information

Entry
Database: PDB / ID: 7u6h
TitleHalD with ornithine and alpha-ketoglutarate
ComponentsHalogenase D
KeywordsBIOSYNTHETIC PROTEIN
Function / homology2-OXOGLUTARIC ACID / NICKEL (II) ION / L-ornithine / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / ArpA protein
Function and homology information
Biological speciesPseudomonas kilonensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsSwenson, C.V. / Neugebauer, M.E. / Kissman, E.N. / Chang, M.C.Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Biocatalytic control of site-selectivity and chain length-selectivity in radical amino acid halogenases.
Authors: Kissman, E.N. / Neugebauer, M.E. / Sumida, K.H. / Swenson, C.V. / Sambold, N.A. / Marchand, J.A. / Millar, D.C. / Chang, M.C.Y.
History
DepositionMar 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 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: Halogenase D
B: Halogenase D
C: Halogenase D
D: Halogenase D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,28132
Polymers123,1224
Non-polymers3,16028
Water13,980776
1
A: Halogenase D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6038
Polymers30,7801
Non-polymers8237
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Halogenase D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7109
Polymers30,7801
Non-polymers9298
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Halogenase D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5158
Polymers30,7801
Non-polymers7357
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Halogenase D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4537
Polymers30,7801
Non-polymers6736
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.050, 73.226, 73.176
Angle α, β, γ (deg.)66.240, 75.800, 85.280
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Halogenase D


Mass: 30780.486 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas kilonensis (bacteria) / Gene: VP02_10785 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0F4XRB2

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Non-polymers , 8 types, 804 molecules

#2: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-ORN / L-ornithine / Ornithine


Type: L-peptide linking / Mass: 132.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 776 / 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: 2.88 Å3/Da / Density % sol: 55.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: Equal volumes of protein solution (PkHalD (6 mg/ml), ornithine (3 mM), alpha-ketoglutarate (3 mM, pH7)) and reservoir solution (MES buffer (100 mM, pH 6.2), 25% (w/v) PEG 550 MME were mixed

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Data collection

DiffractionMean temperature: 194 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 2→69.84 Å / Num. obs: 87446 / % possible obs: 97.5 % / Redundancy: 7.1 % / Biso Wilson estimate: 33.83 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.054 / Rrim(I) all: 0.144 / Net I/σ(I): 8.8 / Num. measured all: 620910 / Scaling rejects: 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.046.52.2762872544140.5070.9562.4721.196.1
10.77-69.847.80.03744815780.9990.0140.0431.199.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSMar 15, 2019data reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NIE

6nie


Resolution: 2→69.837 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 24.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2126 4312 4.93 %
Rwork0.1769 83071 -
obs0.1787 87383 97.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.15 Å2 / Biso mean: 45.0459 Å2 / Biso min: 17.51 Å2
Refinement stepCycle: final / Resolution: 2→69.837 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8261 0 195 776 9232
Biso mean--59.6 50.98 -
Num. residues----1012
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.02270.36121390.3231274096
2.0227-2.04650.35931520.3194270496
2.0465-2.07150.32881450.2974271596
2.0715-2.09770.33391280.2723280596
2.0977-2.12530.30511510.2648265296
2.1253-2.15440.28241470.2447277297
2.1544-2.18520.27681620.2344270696
2.1852-2.21780.24551280.2234278397
2.2178-2.25250.25921280.2176270696
2.2525-2.28940.25761360.2163282597
2.2894-2.32890.27251480.2134269397
2.3289-2.37120.29511390.2109279597
2.3712-2.41690.23731380.2015273897
2.4169-2.46620.26921390.1914277097
2.4662-2.51980.24491510.1865278697
2.5198-2.57840.22321270.1831275597
2.5784-2.64290.23771360.1845277398
2.6429-2.71440.24911470.1831279898
2.7144-2.79430.24061380.1826276898
2.7943-2.88450.21951460.1728279298
2.8845-2.98750.2161380.1752279198
2.9875-3.10720.20711280.1808277498
3.1072-3.24860.21391530.179278898
3.2486-3.41980.22191680.1664279299
3.4198-3.63410.19031460.1537282299
3.6341-3.91470.16031490.1439275899
3.9147-4.30860.17221470.137284099
4.3086-4.93190.15311590.1308279899
4.9319-6.21310.19211490.1622281799
6.2131-69.8370.19211500.1775281599
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)
14.9820.25512.18243.31090.19054.62-0.099-0.2033-0.5768-0.72840.09180.28410.3079-1.00990.09760.4232-0.1336-0.00680.4165-0.0980.550711.2622-4.2664-29.3881
21.5191-0.02320.38631.1732-0.04591.7273-0.0221-0.1505-0.4566-0.0591-0.0068-0.00120.0790.04760.05260.28270.00690.00290.3122-0.02220.341527.55360.6486-23.4177
32.0869-0.72860.75035.0209-2.02763.69690.03960.5897-0.3563-0.7605-0.20190.12830.4359-0.1601-0.10770.3486-0.013-0.05580.6276-0.22270.291115.78625.8738-43.7237
42.5542-0.33660.54570.6597-0.10572.02270.02680.38870.2463-0.1645-0.09360.2488-0.1282-0.22530.0710.28820.06040.00330.3972-0.07790.226918.156119.7591-38.6315
51.0342-0.40760.67881.36810.29351.09360.01760.0141-0.10440.08370.02320.3762-0.2235-0.1746-0.01050.24340.01250.00130.4664-0.06470.310715.576111.4056-27.2072
61.4084-0.1120.57050.6310.35960.95130.09330.3603-0.0354-0.1056-0.1311-0.0408-0.0489-0.1180.04680.27310.02790.00610.3843-0.07580.260128.960814.9963-35.3297
71.90240.18420.45762.14640.45721.06740.066-0.03150.28140.0659-0.1660.0003-0.3629-0.070.11460.26520.02830.01530.2852-0.0370.223234.358423.6703-23.0065
81.3962-0.02330.0551.9567-0.05231.25530.07580.5384-0.1857-0.1744-0.0435-0.02440.0438-0.0221-0.06680.24310.0176-0.00620.4183-0.07630.283230.267112.8167-35.1262
91.21550.49370.37991.6218-1.43891.77350.011-0.41890.21520.3580.16970.1588-0.52210.0291-0.19260.33730.0397-0.01150.4838-0.11420.269516.920617.8033-25.4372
102.50510.46530.35261.74260.32251.7674-0.10570.39090.51550.0230.0315-0.0373-0.7829-0.50620.01620.42870.0748-0.01350.51960.02660.470315.663625.897-36.898
110.17960.0795-1.05730.65180.28956.80430.0219-0.24830.2121-0.1035-0.17170.1446-0.4075-0.64720.00880.43930.0546-0.0390.7561-0.27390.427229.460634.22025.9747
122.0997-0.48180.2184.9155-0.66921.96610.0376-0.23610.45020.4779-0.1362-0.6043-0.2014-0.11030.11940.30290.015-0.01970.5102-0.11270.345535.415325.4598-12.2075
131.5448-0.0924-0.26181.37460.4611.62210.0059-0.8683-0.090.4661-0.09980.06710.1195-0.15850.13110.4644-0.0391-0.01250.8333-0.05190.281732.695816.05898.8604
140.9237-0.6328-0.00611.12660.46951.9034-0.0661-0.7496-0.11780.3470.00860.04610.1380.00260.02580.3342-0.0126-0.00310.55190.04050.244835.66037.86711.0118
154.67371.8564-1.3274.1386-0.91753.55-0.1881-0.35670.4601-0.0956-0.1443-0.5342-0.64630.96370.25140.5335-0.1182-0.11630.6655-0.16680.560374.671730.0371-16.6609
161.01910.14230.1031.2815-0.08391.1389-0.0157-0.61340.18190.16750.020.0325-0.0951-0.01920.01820.31240.0289-0.0290.4007-0.07470.272660.129820.4269-15.8942
172.0888-0.1741-0.34422.7413-0.8091.1660.04550.28930.4228-0.44840.0398-0.1001-0.33310.012-0.12290.32280.0490.0430.2650.03710.381659.057632.6424-38.302
182.1761-0.24641.05292.8513-0.78222.6955-0.0529-0.00410.6756-0.2857-0.257-0.6302-0.18880.27610.22160.325-0.00080.04340.3249-0.03240.499772.253131.4083-34.1465
191.64260.0306-0.67541.11170.38170.36590.04750.0720.2328-0.1571-0.0318-0.1542-0.02010.0899-0.00750.230.0042-0.00330.2479-0.02180.290763.427322.5626-32.5945
201.51190.2378-0.01880.9548-0.10271.20450.19240.07650.45310.1026-0.15740.1334-0.2201-0.1748-0.03850.25130.0220.00480.2781-0.07080.354352.768728.4175-28.0863
211.91610.5335-0.17451.80420.45281.69560.0270.3561-0.1901-0.138-0.00320.07450.1564-0.1011-0.04990.22770.0589-0.03580.2803-0.04920.26649.393610.8377-34.5323
221.21080.2703-0.39560.94420.22091.2410.1087-0.11910.4436-0.01250.01530.0757-0.1861-0.0124-0.07020.24730.0172-0.01720.2789-0.0390.383452.371826.441-29.8683
231.2088-0.0070.87911.4291-0.94711.48120.17690.3944-0.2963-0.3001-0.32620.02910.26650.18950.13430.28180.01180.01040.2891-0.02770.386166.509818.2852-34.7202
243.7253-0.1181-0.11571.90550.54673.00350.03630.57750.7226-0.9533-0.18130.0564-0.1932-0.19480.10110.48590.02870.02870.53610.02210.393163.49626.2374-46.2935
252.057-3.34440.416.3721-0.66990.03720.37810.48580.0899-0.4705-0.6369-0.54410.14050.13120.17680.40330.02130.02990.2831-0.05710.603459.0971-18.7203-36.25
262.34040.2335-0.31211.6209-0.52991.0310.0516-0.4425-0.51660.2191-0.1081-0.24340.2742-0.05050.05120.3885-0.0092-0.01330.29130.08930.526454.6312-11.5967-19.1612
271.42980.36440.0661.55050.40841.3286-0.0033-0.222-0.51550.0342-0.0661-0.50760.36690.17680.12090.31670.05290.01450.31470.07030.624765.0515-14.1652-22.1251
281.17570.1123-0.30311.86470.45640.8988-0.0726-0.4683-0.48810.3277-0.0115-0.32190.2020.18750.07480.33080.0252-0.02430.37750.13280.435857.0957-5.4445-12.337
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 25 )A7 - 25
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 53 )A26 - 53
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 71 )A54 - 71
4X-RAY DIFFRACTION4chain 'A' and (resid 72 through 110 )A72 - 110
5X-RAY DIFFRACTION5chain 'A' and (resid 111 through 139 )A111 - 139
6X-RAY DIFFRACTION6chain 'A' and (resid 140 through 176 )A140 - 176
7X-RAY DIFFRACTION7chain 'A' and (resid 177 through 200 )A177 - 200
8X-RAY DIFFRACTION8chain 'A' and (resid 201 through 227 )A201 - 227
9X-RAY DIFFRACTION9chain 'A' and (resid 228 through 247 )A228 - 247
10X-RAY DIFFRACTION10chain 'A' and (resid 248 through 259 )A248 - 259
11X-RAY DIFFRACTION11chain 'D' and (resid 7 through 25 )D7 - 25
12X-RAY DIFFRACTION12chain 'D' and (resid 26 through 41 )D26 - 41
13X-RAY DIFFRACTION13chain 'D' and (resid 42 through 139 )D42 - 139
14X-RAY DIFFRACTION14chain 'D' and (resid 140 through 259 )D140 - 259
15X-RAY DIFFRACTION15chain 'B' and (resid 8 through 25 )B8 - 25
16X-RAY DIFFRACTION16chain 'B' and (resid 26 through 53 )B26 - 53
17X-RAY DIFFRACTION17chain 'B' and (resid 54 through 92 )B54 - 92
18X-RAY DIFFRACTION18chain 'B' and (resid 93 through 110 )B93 - 110
19X-RAY DIFFRACTION19chain 'B' and (resid 111 through 154 )B111 - 154
20X-RAY DIFFRACTION20chain 'B' and (resid 155 through 176 )B155 - 176
21X-RAY DIFFRACTION21chain 'B' and (resid 177 through 200 )B177 - 200
22X-RAY DIFFRACTION22chain 'B' and (resid 201 through 227 )B201 - 227
23X-RAY DIFFRACTION23chain 'B' and (resid 228 through 247 )B228 - 247
24X-RAY DIFFRACTION24chain 'B' and (resid 248 through 260 )B248 - 260
25X-RAY DIFFRACTION25chain 'C' and (resid 7 through 25 )C7 - 25
26X-RAY DIFFRACTION26chain 'C' and (resid 26 through 92 )C26 - 92
27X-RAY DIFFRACTION27chain 'C' and (resid 93 through 139 )C93 - 139
28X-RAY DIFFRACTION28chain 'C' and (resid 140 through 259 )C140 - 259

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