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- PDB-3b8l: CRYSTAL STRUCTURE OF A PUTATIVE AROMATIC RING HYDROXYLASE (SARO_3... -

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Basic information

Entry
Database: PDB / ID: 3b8l
TitleCRYSTAL STRUCTURE OF A PUTATIVE AROMATIC RING HYDROXYLASE (SARO_3538) FROM NOVOSPHINGOBIUM AROMATICIVORANS DSM AT 1.75 A RESOLUTION
ComponentsUncharacterized protein
KeywordsOXIDOREDUCTASE / PUTATIVE AROMATIC RING HYDROXYLASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologySnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / DI(HYDROXYETHYL)ETHER / SnoaL-like domain-containing protein
Function and homology information
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of NTF2-like protein of unknown function (YP_001165924.1) from Novosphingobium aromaticivorans DSM 12444 at 1.75 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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
C: Uncharacterized protein
D: Uncharacterized protein
E: Uncharacterized protein
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,99919
Polymers111,8446
Non-polymers1,15513
Water17,439968
1
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4899
Polymers55,9223
Non-polymers5676
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
MethodPISA
2
D: Uncharacterized protein
E: Uncharacterized protein
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,51010
Polymers55,9223
Non-polymers5887
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.850, 95.850, 232.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TRIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
Uncharacterized protein


Mass: 18640.736 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria)
Strain: DSM 12444 / Gene: YP_001165924.1, Saro_3538 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A4XEN7
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 968 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsREMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG.

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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: 48.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: NANODROP, 30.0% Glycerol, 5.6% PEG 4000, 0.1M Acetate pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0000, 0.9798, 0.9796
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 30, 2007
RadiationMonochromator: Double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97981
30.97961
ReflectionResolution: 1.75→29.54 Å / Num. obs: 109179 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.44 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 12.12
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.75-1.810.7361.65510518991194.4
1.81-1.890.632.28539122891199.9
1.89-1.970.4463.272745193231100
1.97-2.070.3234.376307201931100
2.07-2.20.2425.879753210511100
2.2-2.370.1827.67984420992199.9
2.37-2.610.12910.580545211231100
2.61-2.990.08315.780429210571100
2.99-3.760.04297901420791199.9
3.76-29.540.02640.47980121004199.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
XDSdata reduction
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→29.54 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.928 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.098
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. GLYCEROL AND POLYETHYLENE GLYCOL WERE MODELED FROM THE CRYSTALLIZATION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.199 5461 5 %RANDOM
Rwork0.167 ---
obs0.169 109062 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.332 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20 Å2
2---0.73 Å20 Å2
3---1.46 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6632 0 74 968 7674
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0217111
X-RAY DIFFRACTIONr_bond_other_d0.0010.024638
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.9349659
X-RAY DIFFRACTIONr_angle_other_deg0.922311215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6675919
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99722.759319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.651151090
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6141552
X-RAY DIFFRACTIONr_chiral_restr0.0920.21065
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028208
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021618
X-RAY DIFFRACTIONr_nbd_refined0.2030.21321
X-RAY DIFFRACTIONr_nbd_other0.2030.25177
X-RAY DIFFRACTIONr_nbtor_refined0.1840.23450
X-RAY DIFFRACTIONr_nbtor_other0.0870.23875
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2710
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1140.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2390.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.238
X-RAY DIFFRACTIONr_mcbond_it0.9011.54766
X-RAY DIFFRACTIONr_mcbond_other0.2251.51846
X-RAY DIFFRACTIONr_mcangle_it1.23227157
X-RAY DIFFRACTIONr_scbond_it2.14732902
X-RAY DIFFRACTIONr_scangle_it3.1834.52502
LS refinement shellResolution: 1.75→1.8 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 378 -
Rwork0.295 7276 -
all-7654 -
obs--96.3 %
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)
12.1378-0.43960.26332.1408-0.20021.12550.11060.3027-0.0393-0.2603-0.06280.2121-0.0441-0.1428-0.0478-0.10970.022-0.0496-0.074-0.0015-0.138826.63659.601520.5051
20.99620.0771-0.08311.7427-0.04411.53550.0117-0.0656-0.20580.1302-0.00510.3410.1304-0.1618-0.0066-0.1195-0.02970.0281-0.11380.0126-0.053826.4098-8.885440.5219
31.2194-0.4336-0.05151.95050.15451.3129-0.0252-0.20110.08490.1473-0.00730.1-0.1531-0.08680.0325-0.09730.0212-0.0056-0.1034-0.0256-0.179233.474316.76845.1824
41.692-0.07260.32282.0535-0.44731.4154-0.016-0.18290.09190.2509-0.0039-0.2752-0.06270.05040.0199-0.1158-0.0037-0.0571-0.1832-0.0078-0.14772.17833.161641.2577
51.37230.3041-0.00211.9144-0.26611.10620.01890.20710.052-0.2587-0.0667-0.0606-0.00810.06440.0478-0.09670.01180.0043-0.13740.0141-0.193767.42524.476814.8581
60.8743-1.03920.33051.74030.15620.86570.0453-0.0479-0.20660.0311-0.04740.12920.1107-0.09510.0022-0.1125-0.008-0.0139-0.18030.0096-0.103864.3846-18.910327.8303
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-2 - 14417 - 163
2X-RAY DIFFRACTION2BB1 - 14420 - 163
3X-RAY DIFFRACTION3CC1 - 14420 - 163
4X-RAY DIFFRACTION4DD1 - 14420 - 163
5X-RAY DIFFRACTION5EE1 - 14420 - 163
6X-RAY DIFFRACTION6FF2 - 14421 - 163

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