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- PDB-5z9j: Identification of the functions of unusual cytochrome p450-like m... -

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Basic information

Entry
Database: PDB / ID: 5z9j
TitleIdentification of the functions of unusual cytochrome p450-like monooxygenases involved in microbial secondary metablism
ComponentsPutative P450-like enzyme
KeywordsOXIDOREDUCTASE / cytochrome p450 / monooxygenase
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Putative P450-like enzyme
Similarity search - Component
Biological speciesStreptomyces himastatinicus ATCC 53653 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsLu, M. / Lin, L. / Zhang, C. / Chen, Y.
CitationJournal: Chembiochem / Year: 2020
Title: Riboflavin Is Directly Involved in the N-Dealkylation Catalyzed by Bacterial Cytochrome P450 Monooxygenases.
Authors: Zhang, C. / Lu, M. / Lin, L. / Huang, Z. / Zhang, R. / Wu, X. / Chen, Y.
History
DepositionFeb 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative P450-like enzyme
B: Putative P450-like enzyme
C: Putative P450-like enzyme
D: Putative P450-like enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,73510
Polymers178,9434
Non-polymers2,7926
Water10,178565
1
A: Putative P450-like enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5153
Polymers44,7361
Non-polymers7802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-25 kcal/mol
Surface area17490 Å2
MethodPISA
2
B: Putative P450-like enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3522
Polymers44,7361
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-23 kcal/mol
Surface area15760 Å2
MethodPISA
3
C: Putative P450-like enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5153
Polymers44,7361
Non-polymers7802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-24 kcal/mol
Surface area17140 Å2
MethodPISA
4
D: Putative P450-like enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3522
Polymers44,7361
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-24 kcal/mol
Surface area16200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.956, 78.469, 97.680
Angle α, β, γ (deg.)78.270, 72.630, 69.460
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Putative P450-like enzyme


Mass: 44735.723 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces himastatinicus ATCC 53653 (bacteria)
Gene: hmtS / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G0LWB2
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE / Tris


Mass: 163.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 565 / 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: 2.17 Å3/Da / Density % sol: 43.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PEG 3350, Bis-Tris hydrochloride, ammonium acetate, NDSB-256

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 92892 / % possible obs: 90.1 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.046 / Rrim(I) all: 0.091 / Χ2: 0.859 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.033.10.38641200.9210.2430.4580.5380.1
2.03-2.073.50.36645960.9320.2220.4290.5589.4
2.07-2.113.50.34646300.8390.2120.4060.62989.7
2.11-2.153.50.29545410.9570.1810.3470.59287.6
2.15-2.23.50.26743140.9540.1630.3140.61983.2
2.2-2.253.60.24246780.9670.1450.2820.69492
2.25-2.313.70.22747480.9670.1350.2640.76292.1
2.31-2.373.70.1947640.9750.1130.2210.69292.1
2.37-2.443.70.17347220.9780.1020.2010.71791.8
2.44-2.523.70.16147560.9770.0960.1880.78392.8
2.52-2.613.70.14247760.9830.0840.1650.83791.5
2.61-2.713.70.12747410.9870.0760.1480.87691.6
2.71-2.843.60.11143280.9880.0670.130.94384.5
2.84-2.993.80.10148070.9870.060.1180.93393.8
2.99-3.173.80.09148820.9910.0530.1050.9694.6
3.17-3.423.80.0848310.9920.0470.0931.10893.7
3.42-3.763.80.06947540.9940.0410.081.18592
3.76-4.313.60.06343960.9930.0380.0731.28785.6
4.31-5.433.80.05848170.9950.0340.0671.20693.5
5.43-503.80.05446910.9960.0320.0631.05190.9

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-3000data scaling
PDB_EXTRACT3.24data extraction
DENZOdata reduction
PHASERphasing
RefinementResolution: 2→46.329 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0.09 / Phase error: 30.82
RfactorNum. reflection% reflection
Rfree0.2616 1874 2.15 %
Rwork0.222 --
obs0.2228 87214 83.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 121.99 Å2 / Biso mean: 43.58 Å2 / Biso min: 9.95 Å2
Refinement stepCycle: final / Resolution: 2→46.329 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11727 0 194 565 12486
Biso mean--26.81 40.76 -
Num. residues----1523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01312204
X-RAY DIFFRACTIONf_angle_d1.47816657
X-RAY DIFFRACTIONf_chiral_restr0.0661839
X-RAY DIFFRACTIONf_plane_restr0.0092177
X-RAY DIFFRACTIONf_dihedral_angle_d14.1354443
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.0370.482970.3716455558
2.037-2.0970.3841350.33584175
2.097-2.16470.30521200.2945591675
2.1647-2.2420.3061370.2702629981
2.242-2.33180.29211490.2555663684
2.3318-2.43790.28071470.2453678587
2.4379-2.56640.28311500.2375693388
2.5664-2.72720.27111520.2393695289
2.7272-2.93770.27021550.2285680887
2.9377-3.23330.28341510.2322733094
3.2333-3.7010.23831640.1979724892
3.701-4.66220.22611530.1783693688
4.6622-46.3290.23171640.2057710191
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)
11.5848-0.4851-0.3452.00920.87522.46450.1524-0.05320.1053-0.00190.0018-0.0878-0.1642-0.0047-0.12950.24940.0070.00370.23890.06750.2383-16.497315.679314.1464
20.1097-0.04260.20920.4860.22180.62610.2197-0.1721-0.3223-0.06090.09740.23250.3452-0.5482-0.27670.62260.0368-0.00110.73460.14290.7872-14.42455.15422.7435
30.9937-0.0803-0.61081.29870.39492.02250.08810.00280.07040.0058-0.022-0.0224-0.1296-0.0941-0.06020.21820.0324-0.020.22220.05050.2538-15.701214.035510.7687
41.8382-0.1105-0.44152.19080.67571.6978-0.1477-0.06240.01860.10370.09860.02640.24370.02670.06520.285-0.03160.0480.24230.06720.1655-29.0255-20.019914.7519
51.3501-0.25290.12631.39550.32531.3046-0.02710.33860.06760.76770.44210.50370.59320.2477-0.27111.13570.1343-0.09320.57150.06351.0208-16.896-30.536223.6794
62.1138-0.8583-0.52332.28740.57651.696-0.213-0.00350.08250.04460.0988-0.06810.06490.02050.12340.2648-0.03120.02360.23120.07480.2312-29.189-18.480810.9525
71.1546-0.2763-1.04471.46761.17991.4156-0.33170.389-0.2174-0.09390.08460.35870.2398-0.20190.19720.4311-0.07220.04770.36940.00820.3431-34.178-24.42952.8828
82.00970.2466-0.59271.4021-0.62962.17490.3339-0.19160.26410.0498-0.11520.0679-0.18010.139-0.16250.2988-0.05630.04280.2253-0.09190.245-5.2757-30.8373-31.6678
91.43030.8686-0.23571.1108-1.26822.8750.21640.16180.2447-0.15280.1207-0.0585-0.1545-0.0727-0.35410.53580.04030.07880.5091-0.01860.6747-15.6495-26.6325-43.5952
101.42750.0994-0.86791.3528-0.51651.85340.2782-0.37730.08320.25-0.1487-0.0427-0.17150.4127-0.11890.3434-0.13370.02350.361-0.10470.2762-3.566-34.2046-23.2806
112.09040.3832-0.79021.727-0.20861.5676-0.10060.0674-0.0052-0.1256-0.0272-0.080.0709-0.00380.09990.2240.0312-0.05340.2131-0.03780.17598.88637.8091-32.3772
120.0353-0.06120.00850.0656-0.00280.01220.41590.1813-0.84510.2984-0.1454-0.22050.3320.0090.03761.177-0.0327-0.35920.5494-0.14590.8539-6.59561.3326-37.4003
131.7729-1.0250.09150.681-0.09230.0612-0.03850.6732-0.2723-0.52540.2994-0.16730.426-0.0563-0.02790.6446-0.1223-0.180.66160.01780.8171-8.16212.2193-43.8198
142.15450.6443-0.6791.8866-0.34281.7006-0.1123-0.08980.02280.0191-0.0118-0.0638-0.03380.07210.13260.19850.0461-0.08650.2145-0.02720.24439.74638.6869-25.8604
150.3973-0.0810.29961.28140.71070.6735-0.55210.0947-0.82380.0835-0.114-0.3480.4397-0.17130.52840.3768-0.02480.15540.2482-0.04380.53865.2019-10.0783-23.7473
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 145 )A7 - 145
2X-RAY DIFFRACTION2chain 'A' and (resid 146 through 171 )A146 - 171
3X-RAY DIFFRACTION3chain 'A' and (resid 172 through 397 )A172 - 397
4X-RAY DIFFRACTION4chain 'B' and (resid 9 through 146 )B9 - 146
5X-RAY DIFFRACTION5chain 'B' and (resid 147 through 202 )B147 - 202
6X-RAY DIFFRACTION6chain 'B' and (resid 203 through 317 )B203 - 317
7X-RAY DIFFRACTION7chain 'B' and (resid 318 through 398 )B318 - 398
8X-RAY DIFFRACTION8chain 'C' and (resid 7 through 145 )C7 - 145
9X-RAY DIFFRACTION9chain 'C' and (resid 146 through 223 )C146 - 223
10X-RAY DIFFRACTION10chain 'C' and (resid 224 through 398 )C224 - 398
11X-RAY DIFFRACTION11chain 'D' and (resid 9 through 142 )D9 - 142
12X-RAY DIFFRACTION12chain 'D' and (resid 143 through 180 )D143 - 180
13X-RAY DIFFRACTION13chain 'D' and (resid 181 through 202 )D181 - 202
14X-RAY DIFFRACTION14chain 'D' and (resid 203 through 367 )D203 - 367
15X-RAY DIFFRACTION15chain 'D' and (resid 368 through 398 )D368 - 398

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