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- PDB-2oa1: Crystal Structure of RebH, a FAD-dependent halogenase from Lechev... -

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Basic information

Entry
Database: PDB / ID: 2oa1
TitleCrystal Structure of RebH, a FAD-dependent halogenase from Lechevalieria aerocolonigenes, the L-Tryptophan with FAD complex
ComponentsTryptophan halogenase
KeywordsBIOSYNTHETIC PROTEIN / FLAVOPROTEIN / RebH / Rebeccamycin / halogenase / flavin
Function / homology
Function and homology information


tryptophan 7-halogenase / monooxygenase activity / nucleotide binding
Similarity search - Function
Flavin-dependent tryptophan halogenase / Flavin-dependent halogenase / Tryptophan halogenase / : / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
ADENOSINE / FLAVIN-ADENINE DINUCLEOTIDE / TRYPTOPHAN / Tryptophan 7-halogenase RebH
Similarity search - Component
Biological speciesLechevalieria aerocolonigenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 2O9Z / Resolution: 2.15 Å
AuthorsBitto, E. / Bingman, C.A. / Singh, S. / Phillips Jr., G.N.
CitationJournal: Proteins / Year: 2008
Title: The structure of flavin-dependent tryptophan 7-halogenase RebH.
Authors: Bitto, E. / Huang, Y. / Bingman, C.A. / Singh, S. / Thorson, J.S. / Phillips Jr., G.N.
History
DepositionDec 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tryptophan halogenase
B: Tryptophan halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,5777
Polymers125,0802
Non-polymers1,4975
Water19,0241056
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-35 kcal/mol
Surface area38410 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)114.492, 114.492, 231.935
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-2141-

HOH

21B-2065-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 4 / Auth seq-ID: 12 - 528 / Label seq-ID: 32 - 548

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Tryptophan halogenase / Putative halogenase of tryptophan / Halogenase


Mass: 62540.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lechevalieria aerocolonigenes (bacteria)
Strain: 39243 / Gene: rbmJ, rebH / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8KHZ8

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Non-polymers , 5 types, 1061 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1056 / Source method: isolated from a natural source / Formula: H2O

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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: 3.5 Å3/Da / Density % sol: 64.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Protein Solution (18 mg/ml protein, 0.050 M sodium chloride, 0.010 M TRIS pH 8.0) mixed in a 1:1 ratio with the Well Solution (0.9 M K2HPO4, 0.5 M NaH2PO4) crystals soaked for 22 hours in ...Details: Protein Solution (18 mg/ml protein, 0.050 M sodium chloride, 0.010 M TRIS pH 8.0) mixed in a 1:1 ratio with the Well Solution (0.9 M K2HPO4, 0.5 M NaH2PO4) crystals soaked for 22 hours in solution of 0.6 M K2HPO4, 0.33 M NaH2PO4, ~0.005 M FAD, ~0.003 M L-tryptophan, 0.030 M NaCl, Cryoprotected with: well solution supplemented with up to 30% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97931 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 18, 2006 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochromater / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.15→49.576 Å / Num. obs: 92078 / % possible obs: 98.8 % / Redundancy: 20.4 % / Rmerge(I) obs: 0.102 / Χ2: 1.013 / Net I/σ(I): 24.905
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.15-2.29.40.5343.62856341.00890.9
2.2-2.2611.60.52958970.98295.4
2.26-2.3214.20.50660990.9998.5
2.32-2.3817.20.48162290.97999.7
2.38-2.4620.40.44461250.96499.6
2.46-2.5522.50.39561970.97399.7
2.55-2.6523.30.31861830.97899.8
2.65-2.7723.40.23861790.98199.8
2.77-2.9223.40.17961820.97699.9
2.92-3.123.40.13762160.98199.8
3.1-3.3423.40.09961941.13299.9
3.34-3.6823.40.07762151.14699.9
3.68-4.2123.40.05862021.04999.9
4.21-5.323.20.04962340.96699.9
5.3-49.5822.90.0562921.04699.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: 2O9Z
Starting model: apo form of same protein in same lattice

Resolution: 2.15→19.952 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.178 / WRfactor Rwork: 0.139 / SU B: 7.782 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.194 4630 5.037 %RANDOM
Rwork0.152 ---
obs0.154 91914 98.846 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 38.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.031 Å20.015 Å20 Å2
2--0.031 Å20 Å2
3----0.046 Å2
Refinement stepCycle: LAST / Resolution: 2.15→19.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8468 0 103 1056 9627
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228813
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.94411974
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17151052
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39523.217460
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.511151372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3971574
X-RAY DIFFRACTIONr_chiral_restr0.0980.21241
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026946
X-RAY DIFFRACTIONr_nbd_refined0.1940.24112
X-RAY DIFFRACTIONr_nbtor_refined0.3040.26019
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2872
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2450.227
X-RAY DIFFRACTIONr_mcbond_it0.7251.55389
X-RAY DIFFRACTIONr_mcangle_it1.15728444
X-RAY DIFFRACTIONr_scbond_it2.08633980
X-RAY DIFFRACTIONr_scangle_it3.394.53530
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4228 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.260.5
MEDIUM THERMAL0.832
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.2050.3622790.2595938683390.985
2.205-2.2650.2883220.2335997659195.873
2.265-2.330.2523380.2076069648898.752
2.33-2.4010.2323180.1945900624199.631
2.401-2.4780.2292930.1825756606899.687
2.478-2.5640.2053110.1765558588399.762
2.564-2.6590.2052610.1735417568899.824
2.659-2.7650.2113160.1625106543599.761
2.765-2.8860.2272550.165019527999.905
2.886-3.0230.1992670.1564747501999.9
3.023-3.1830.2122380.1474561480299.938
3.183-3.3710.1872120.1394310452499.956
3.371-3.5960.1812130.1314052426699.977
3.596-3.8740.172010.1283773397599.975
3.874-4.2280.1471820.1183507369099.973
4.228-4.70.1431510.1133179333299.94
4.7-5.3780.1651790.1252789296999.966
5.378-6.470.2021130.15724462559100
6.47-8.7040.1721170.15319132030100
8.704-19.9520.144640.1331247131599.696
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)
12.59811.09041.44311.37710.61212.20370.1453-0.2062-0.16330.2642-0.14070.05690.4417-0.1457-0.0047-0.0864-0.05980.0615-0.13850.0076-0.1323-21.785724.17055.9291
23.2228-0.68231.56692.5824-1.30068.1594-0.04980.1853-0.4997-0.2235-0.0297-0.29980.48620.07310.0795-0.0089-0.05580.068-0.0051-0.1149-0.0746-23.471318.595-24.3333
32.05790.82441.23211.08220.83822.084-0.01480.0692-0.21360.1044-0.0869-0.02670.58970.01210.10170.0134-0.05650.0732-0.1526-0.0206-0.0782-23.237315.1988-1.5985
40.9466-0.31241.85451.3971-0.83195.93250.058-0.18330.10830.4057-0.11090.0061-0.38240.07150.0529-0.1296-0.07910.0297-0.093-0.0182-0.1369-15.538245.611218.0693
50.7716-0.22050.12665.522-1.5212.6472-0.0193-0.0801-0.09480.59710.0340.60460.2284-0.4107-0.0147-0.0931-0.14220.12-0.0475-0.0277-0.0671-39.567825.01276.9906
61.06330.78930.52751.99960.35061.93320.0064-0.07740.03980.0222-0.05870.08650.12030.03560.0523-0.2291-0.03150.0058-0.14260.0048-0.1926-15.836439.10493.5485
72.09280.51590.31630.8820.14622.3764-0.09710.41770.326-0.06820.06110.2182-0.1214-0.1520.036-0.1906-0.04370.0145-0.05120.0041-0.1012-32.44936.5597-10.3402
83.46110.91574.46230.7685-0.2999.9130.01450.0946-0.11540.1011-0.1487-0.29420.48610.29810.1341-0.1045-0.03190.03790.0474-0.043-0.03-15.298525.8406-13.1942
91.2986-0.0487-0.51640.1831-0.0125.5488-0.18150.4068-0.1409-0.08650.11110.01610.73870.15310.0704-0.0439-0.10690.03590.0079-0.0902-0.1069-26.205820.4125-23.5666
103.3785-0.5961.079810.4494-0.983710.9715-0.23170.2953-0.87830.0328-0.10850.21671.8720.34550.34020.088-0.00180.14990.0284-0.10140.0779-26.29152.1567-3.1619
115.6978-0.66512.33320.96270.14962.6205-0.0150.5184-0.0021-0.1358-0.0791-0.04970.13830.00430.0941-0.21520.00780.01810.013-0.0716-0.1514-6.727430.0661-42.1759
122.9591.40970.83152.6730.75662.16550.08660.0678-0.24480.11110.0634-0.17780.21610.3549-0.1499-0.31560.0491-0.0005-0.03010.0324-0.157915.843836.4153-26.9981
136.29382.921.98826.6941.44555.0025-0.0248-0.4558-0.34320.22140.0158-0.00550.40840.12490.009-0.16940.02290.03160.00940.0784-0.15718.74733.3114-3.8491
142.2639-0.37920.74150.41020.05481.4470.0750.3598-0.0477-0.0499-0.1182-0.01230.15090.03130.0432-0.2545-0.03130.0438-0.03620.0078-0.1228-1.973635.0334-38.077
151.6847-0.1242-0.08392.0410.19052.42260.06970.37960.1462-0.1916-0.0836-0.0179-0.09920.18460.014-0.3088-0.029300.05850.0378-0.163115.717645.9428-37.2621
163.7968-0.04250.73620.92840.00881.7116-0.00570.08560.11740.0615-0.03860.03680.0489-0.12680.0442-0.2809-0.01710.0211-0.0477-0.0225-0.1691-11.539739.6865-33.2361
172.12110.1327-0.27460.0461-0.27891.85010.1404-0.28630.36320.0853-0.10170.2653-0.148-0.0542-0.0387-0.2334-0.00540.0342-0.0381-0.0042-0.09773.269750.741-20.0174
183.61441.67034.29531.02192.9188.58610.1317-0.0115-0.17260.2026-0.25810.26050.6036-0.04710.1264-0.1306-0.04910.03550.01950.0478-0.0427-2.597530.7055-16.3655
190.76270.3516-1.06890.58290.26873.14590.0768-0.3669-0.09870.1219-0.11190.01870.40330.2140.035-0.2021-0.0034-0.01180.04820.0623-0.11628.438734.91-6.3259
205.05810.3894-2.31217.89451.180712.9512-0.06790.0129-0.6652-0.2717-0.1175-0.53941.71660.48490.1854-0.0820.13710.079-0.03780.05440.059121.273820.4998-27.0163
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA12 - 12032 - 140
22AA121 - 138141 - 158
33AA139 - 199159 - 219
44AA200 - 254220 - 274
55AA255 - 336275 - 356
66AA337 - 398357 - 418
77AA399 - 446419 - 466
88AA447 - 473467 - 493
99AA474 - 517494 - 537
1010AA518 - 528538 - 548
1111BB12 - 7532 - 95
1212BB76 - 12296 - 142
1313BB123 - 140143 - 160
1414BB141 - 254161 - 274
1515BB255 - 337275 - 357
1616BB338 - 400358 - 420
1717BB401 - 446421 - 466
1818BB447 - 472467 - 492
1919BB473 - 517493 - 537
2020BB518 - 528538 - 548

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