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- PDB-3rh7: Crystal structure of a putative oxidoreductase (SMa0793) from Sin... -

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Basic information

Entry
Database: PDB / ID: 3rh7
TitleCrystal structure of a putative oxidoreductase (SMa0793) from Sinorhizobium meliloti 1021 at 3.00 A resolution
ComponentsHypothetical oxidoreductase
KeywordsOXIDOREDUCTASE / FMN-binding split barrel / Nudix / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-biology
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-NH group of donors; With NAD+ or NADP+ as acceptor / riboflavin reductase (NADPH) activity / FMN binding
Similarity search - Function
: / Flavin reductase like domain / Flavin reductase like domain / Flavin reductase like domain / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Roll ...: / Flavin reductase like domain / Flavin reductase like domain / Flavin reductase like domain / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Roll / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Probable flavin reductase
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Hypothetical oxidoreductase (SMa0793) from SINORHIZOBIUM MELILOTI 1021 at 3.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Nov 16, 2011Group: Structure summary
Revision 1.4Dec 24, 2014Group: Structure summary
Revision 1.5Nov 8, 2017Group: Refinement description / Category: software
Revision 1.6Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical oxidoreductase
B: Hypothetical oxidoreductase
C: Hypothetical oxidoreductase
D: Hypothetical oxidoreductase
E: Hypothetical oxidoreductase
F: Hypothetical oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,40710
Polymers205,5816
Non-polymers1,8254
Water00
1
A: Hypothetical oxidoreductase
B: Hypothetical oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9833
Polymers68,5272
Non-polymers4561
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-67 kcal/mol
Surface area23030 Å2
MethodPISA
2
C: Hypothetical oxidoreductase
D: Hypothetical oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4404
Polymers68,5272
Non-polymers9132
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7800 Å2
ΔGint-73 kcal/mol
Surface area22250 Å2
MethodPISA
3
E: Hypothetical oxidoreductase
F: Hypothetical oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9833
Polymers68,5272
Non-polymers4561
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-67 kcal/mol
Surface area22940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.920, 99.735, 234.302
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Hypothetical oxidoreductase


Mass: 34263.555 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: RA0429, SMa0793 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q92ZM6
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (-9), FOLLOWED BY THE TARGET SEQUENCE. CLONING WAS BASED ON VERSION 1 OF THE SMA0793 GENE FROM SINORHIZOBIUM MELILOTI 1021 (UNIPROTKB Q92ZM6 VERSION 1 / REFSEQ NP_435675.1) AND THE EXPRESSED CONSTRUCT CONTAINS NINE RESIDUES (-8)MADFQGETE(0) AT THE N-TERMINUS NOT PRESENT IN THE CURRENT PREDICTED GENE PRODUCT (VERSION 2 OF UNIPROTKB Q92ZM6 / REFSEQ NP_435675.2).

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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: 2.61 Å3/Da / Density % sol: 52.91 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R MERGE, COMPLETENESS AND
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.2M LiAcetate, 20.0% PEG-3350, No Buffer pH 7.8, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9796,0.9611,0.9794
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2011
Details: Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.96111
30.97941
ReflectionResolution: 3→29.759 Å / Num. obs: 42960 / % possible obs: 94.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 78.394 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 10.57
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
3-3.110.5151.514588799593.3
3.11-3.230.3812.114100771696
3.23-3.380.265314480807394.9
3.38-3.550.1864.213015747993.8
3.55-3.780.1335.915330834597.1
3.78-4.060.0858.714168761594.9
4.06-4.470.05213.514321785793.1
4.47-5.110.0391714435793395
5.11-6.40.0417.614474777894
6.40.01832.314497788591.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 6, 2010data scaling
BUSTER-TNT2.8.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 3→29.759 Å / Cor.coef. Fo:Fc: 0.9305 / Cor.coef. Fo:Fc free: 0.9062 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. 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 FOR THE REDUCED ...Details: 1. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. FMN WAS MODELED IN FOUR SUBUNITS BASED ON THE DENSITY AND COMPARISON WITH RELATED STRUCTURES. THERE IS SOME UNMODELLED DENSITY NEAR THE MODELED FMN. FMN MAY BE PARTIALLY PRESENT IN THE OTHER TWO SUBUNITS (B/E), BUT IT WAS NOT MODELED. FMN MODELED COULD REPRESENT (ORDERED) PART OF FAD AS SEEN IN OTHER HOMOLOGS. 4. NCS RESTRAINTS WERE APPLIED USING BUSTERS LSSR RESTRAINT REPRESENTATION (-AUTONCS).
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 2158 5.03 %RANDOM
Rwork0.1867 ---
obs0.1887 42920 --
Displacement parametersBiso max: 188.26 Å2 / Biso mean: 79.5308 Å2 / Biso min: 25.68 Å2
Baniso -1Baniso -2Baniso -3
1-12.6177 Å20 Å20 Å2
2---21.4773 Å20 Å2
3---8.8596 Å2
Refinement stepCycle: LAST / Resolution: 3→29.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12763 0 124 0 12887
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5904SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes338HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2073HARMONIC5
X-RAY DIFFRACTIONt_it13147HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion16HARMONIC0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1741SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14958SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d13147HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg17906HARMONIC21.17
X-RAY DIFFRACTIONt_omega_torsion3.07
X-RAY DIFFRACTIONt_other_torsion2.83
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3034 145 4.73 %
Rwork0.2524 2921 -
all0.2548 3066 -
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)
10.9493-0.2131-0.10372.0077-0.35011.06810.01690.1223-0.086-0.0911-0.06530.2350.3795-0.32750.0485-0.1242-0.04950.0060.20050.0008-0.177161.439921.614497.972
21.36060.6913-0.63461.3318-0.45691.81730.0581-0.2573-0.01260.2477-0.0893-0.13960.09770.11510.0312-0.11140.0353-0.01930.13850.0421-0.131978.17829.9177108.315
31.4141-0.3695-0.55351.3772-0.17873.1094-0.2461-0.0677-0.30150.31920.190.40710.5869-0.21190.0561-0.04240.03180.0889-0.0865-0.047-0.073674.8461-10.037256.9994
41.1923-0.3493-1.18311.31140.71172.97850.0398-0.37950.17470.35040.3283-0.2268-0.13420.6917-0.3681-0.0944-0.0019-0.02790.087-0.1716-0.091691.86063.011158.1388
51.17920.15370.09052.48340.41150.7076-0.0526-0.08490.5377-0.0873-0.0818-0.2187-0.35650.29880.1344-0.1462-0.0548-0.0723-0.039-0.04170.147148.1124-23.449893.1398
61.60610.60580.60122.14960.56332.2330.0368-0.49640.53590.61760.03830.163-0.2821-0.33-0.0751-0.1190.11810.05290.0358-0.22830.028131.3565-28.8511105.037
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|8 - 321 }A8 - 321
2X-RAY DIFFRACTION2{ B|14 - 299 }B14 - 299
3X-RAY DIFFRACTION3{ C|14 - 321 }C14 - 321
4X-RAY DIFFRACTION4{ D|14 - 321 }D14 - 321
5X-RAY DIFFRACTION6{ F|14 - 321 }F14 - 321

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