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- PDB-6c3b: O2-, PLP-Dependent L-Arginine Hydroxylase RohP Holoenzyme -

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Basic information

Entry
Database: PDB / ID: 6c3b
TitleO2-, PLP-Dependent L-Arginine Hydroxylase RohP Holoenzyme
ComponentsUncharacterized protein
KeywordsBIOSYNTHETIC PROTEIN / O2- / PLP-dependent L-arginine hydroxylase
Function / homologybiosynthetic process / Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / pyridoxal phosphate binding / TRIETHYLENE GLYCOL / Aminotransferase class I/classII large domain-containing protein
Function and homology information
Biological speciesStreptomyces cattleya (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsHedges, J.B. / Ryan, K.S.
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Snapshots of the Catalytic Cycle of an O2, Pyridoxal Phosphate-Dependent Hydroxylase.
Authors: Hedges, J.B. / Kuatsjah, E. / Du, Y.L. / Eltis, L.D. / Ryan, K.S.
History
DepositionJan 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 4, 2023Group: 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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,34319
Polymers95,0242
Non-polymers1,31917
Water14,916828
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint40 kcal/mol
Surface area25750 Å2
Unit cell
Length a, b, c (Å)79.380, 112.410, 102.160
Angle α, β, γ (deg.)90.000, 95.770, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-668-

HOH

21B-845-

HOH

31B-929-

HOH

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Components

#1: Protein Uncharacterized protein


Mass: 47511.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cattleya (strain ATCC 35852 / DSM 46488 / JCM 4925 / NBRC 14057 / NRRL 8057) (bacteria)
Strain: ATCC 35852 / DSM 46488 / JCM 4925 / NBRC 14057 / NRRL 8057
Gene: SCATT_03970 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G8WNK6*PLUS
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 828 / 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: 2.39 Å3/Da / Density % sol: 48.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M sodium malonate pH 7, 16-20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.51→56.69 Å / Num. obs: 139369 / % possible obs: 100 % / Redundancy: 4.2 % / Biso Wilson estimate: 14.15 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.044 / Rrim(I) all: 0.09 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1 / Redundancy: 4 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.51-1.540.77969310.660.440.89899.9
8.27-56.690.0360.9960.0210.04298.5

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimless0.5.23data scaling
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DJ1

5dj1


Resolution: 1.51→56.686 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.68
RfactorNum. reflection% reflection
Rfree0.1725 7175 5.15 %
Rwork0.1522 --
obs0.1533 139353 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 73.77 Å2 / Biso mean: 21.9022 Å2 / Biso min: 7.04 Å2
Refinement stepCycle: final / Resolution: 1.51→56.686 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5855 0 80 828 6763
Biso mean--34.22 33.36 -
Num. residues----728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066172
X-RAY DIFFRACTIONf_angle_d0.8738382
X-RAY DIFFRACTIONf_chiral_restr0.052932
X-RAY DIFFRACTIONf_plane_restr0.0061071
X-RAY DIFFRACTIONf_dihedral_angle_d7.7325019
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.51-1.52720.26912340.252244654699
1.5272-1.54510.24352450.230543314576
1.5451-1.5640.23232180.218644604678
1.564-1.58380.23612280.210443794607
1.5838-1.60460.23052410.206143814622
1.6046-1.62660.23142430.189643714614
1.6266-1.64980.21282740.186643864660
1.6498-1.67450.2012370.179143894626
1.6745-1.70060.21732530.181243334586
1.7006-1.72850.20482090.171744744683
1.7285-1.75830.19432320.171844214653
1.7583-1.79030.19372420.16543414583
1.7903-1.82470.19162440.167144084652
1.8247-1.8620.18892510.15644184669
1.862-1.90250.18822440.148943684612
1.9025-1.94670.16922490.14843704619
1.9467-1.99540.15382370.148843994636
1.9954-2.04940.20342100.147644204630
2.0494-2.10970.17072290.136644144643
2.1097-2.17780.1622480.139143954643
2.1778-2.25560.16342360.142644254661
2.2556-2.34590.15912450.147244224667
2.3459-2.45270.1692340.152744114645
2.4527-2.5820.17612170.150444144631
2.582-2.74380.1722530.151844214674
2.7438-2.95560.17782540.15243584612
2.9556-3.2530.15982440.142544264670
3.253-3.72370.1582330.137144394672
3.7237-4.69110.12782340.121344694703
4.6911-56.7260.15562570.151244704727
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)
13.15260.3114-0.2320.5876-0.14850.9280.03810.2895-0.1201-0.2443-0.1568-0.02060.0355-0.00760.10810.23380.11330.02460.22480.00390.1315-4.722449.3168.5628
20.9209-0.044-0.12660.5996-0.21810.76060.04050.032-0.0282-0.0642-0.0284-0.0144-0.0037-0.0013-0.00450.09560.0469-0.00970.0806-0.00410.1073-14.416751.387831.0594
31.5387-0.91510.97570.6503-0.52440.64950.0286-0.1761-0.01090.04160.15830.2366-0.0867-0.43-0.11080.0950.0622-0.00050.220.03590.1864-31.533653.586638.3674
41.4173-1.271-0.44913.01890.47681.46170.00180.02470.0005-0.066-0.00530.1511-0.1658-0.1550.02150.09170.0446-0.01260.112-0.00340.1309-28.531758.428430.117
51.1883-0.23160.38511.6457-1.01711.32270.09310.15450.0656-0.1643-0.03730.1208-0.1082-0.1282-0.06090.14130.0741-0.01470.12440.00730.1289-21.81458.316826.1124
60.9875-0.6042-0.21491.13930.06291.17690.04140.07950.0717-0.0511-0.0671-0.0077-0.04690.00810.02950.10270.0266-0.00110.07530.00740.1042-10.173555.255230.1766
78.033-2.57294.80512.947-2.68083.49950.0260.20990.2655-0.1698-0.095-0.0533-0.1408-0.03520.07250.19450.08420.03690.180.0270.0892-6.038357.884312.5708
83.1040.92640.54841.81760.06442.17080.1060.5211-0.2156-0.3677-0.06670.19410.175-0.4268-0.03710.25320.0801-0.09330.3033-0.04910.2018-29.311948.20388.8822
90.70070.33050.19410.75290.53670.91410.01630.1567-0.494-0.1597-0.0290.10610.8169-0.38090.09670.4151-0.0472-0.07410.2493-0.1130.4044-30.793133.810917.4139
103.24051.64340.50513.01211.53854.39380.0490.4899-0.3422-0.4373-0.07270.26450.4107-0.18310.04810.32640.083-0.10550.2804-0.11510.312-27.449238.2659.5122
112.32720.28972.17320.47470.47943.00880.05950.22360.0741-0.1469-0.1238-0.1223-0.0340.15580.07520.23080.10430.04390.21250.06890.15549.150246.914713.7196
120.7146-0.0898-0.17580.6271-0.29231.2540.05620.1528-0.0602-0.1765-0.06030.02570.09-0.03480.00670.13960.0525-0.03220.1071-0.01760.1198-0.756130.803223.9282
132.716-0.8764-0.3881.84990.42371.27890.0091-0.09640.04930.040.0093-0.07180.0460.0884-0.01080.08150.0206-0.01430.0970.00580.07517.543131.770245.6505
140.9215-0.0308-0.45213.8645-0.03360.91850.02840.0042-0.1248-0.1219-0.0622-0.07510.13540.11250.03350.10740.0526-0.01850.09860.00440.106414.375824.304237.7404
151.1618-0.1184-0.121.9867-0.34191.10150.06950.0925-0.0716-0.1025-0.0973-0.17730.02050.18170.0330.10690.0582-0.0070.12430.00270.109812.237728.117631.0472
161.3771-0.43-0.45065.82070.58691.47010.06740.0567-0.0885-0.0976-0.11550.02450.07730.03560.05170.1180.0544-0.02780.0874-0.0170.10674.073622.756831.6611
171.09810.1036-0.27740.5197-0.16460.85380.05810.184-0.0555-0.1629-0.0894-0.02320.06030.03560.02910.1510.0696-0.00870.1332-0.0030.10261.995835.581421.4372
181.9780.97391.19441.31990.81212.34380.04270.15020.1469-0.1799-0.0453-0.2631-0.08810.4052-0.03840.12070.04830.05770.22410.04120.228227.080242.924330.5213
191.2980.4104-0.39781.9166-0.28891.81530.1651-0.05090.2860.0188-0.0738-0.1142-0.25340.1962-0.08010.1053-0.00780.01760.11930.00650.162419.352350.226441.9656
207.77012.18660.53776.87480.70518.25040.1736-0.08340.7759-0.29240.1574-0.4005-0.50770.4842-0.25170.1666-0.03390.10240.21990.02320.379928.320156.272532.171
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 59 )A28 - 59
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 143 )A60 - 143
3X-RAY DIFFRACTION3chain 'A' and (resid 144 through 163 )A144 - 163
4X-RAY DIFFRACTION4chain 'A' and (resid 164 through 190 )A164 - 190
5X-RAY DIFFRACTION5chain 'A' and (resid 191 through 215 )A191 - 215
6X-RAY DIFFRACTION6chain 'A' and (resid 216 through 269 )A216 - 269
7X-RAY DIFFRACTION7chain 'A' and (resid 270 through 288 )A270 - 288
8X-RAY DIFFRACTION8chain 'A' and (resid 289 through 321 )A289 - 321
9X-RAY DIFFRACTION9chain 'A' and (resid 322 through 358 )A322 - 358
10X-RAY DIFFRACTION10chain 'A' and (resid 359 through 388 )A359 - 388
11X-RAY DIFFRACTION11chain 'B' and (resid 27 through 59 )B27 - 59
12X-RAY DIFFRACTION12chain 'B' and (resid 60 through 108 )B60 - 108
13X-RAY DIFFRACTION13chain 'B' and (resid 109 through 163 )B109 - 163
14X-RAY DIFFRACTION14chain 'B' and (resid 164 through 190 )B164 - 190
15X-RAY DIFFRACTION15chain 'B' and (resid 191 through 215 )B191 - 215
16X-RAY DIFFRACTION16chain 'B' and (resid 216 through 232 )B216 - 232
17X-RAY DIFFRACTION17chain 'B' and (resid 233 through 288 )B233 - 288
18X-RAY DIFFRACTION18chain 'B' and (resid 289 through 321 )B289 - 321
19X-RAY DIFFRACTION19chain 'B' and (resid 322 through 373 )B322 - 373
20X-RAY DIFFRACTION20chain 'B' and (resid 374 through 390 )B374 - 390

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