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- PDB-3pm9: Crystal structure of a Putative dehydrogenase (RPA1076) from Rhod... -

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Basic information

Entry
Database: PDB / ID: 3pm9
TitleCrystal structure of a Putative dehydrogenase (RPA1076) from Rhodopseudomonas palustris CGA009 at 2.57 A resolution
ComponentsPutative oxidoreductase
KeywordsOXIDOREDUCTASE / PUTATIVE D-2-HYDROXYGLUTARATE DEHYDROGENASE / PUTATIVE D-LACTATE DEHYDROGENASE / FAD-BINDING/TRANSPORTER-ASSOCIATED DOMAIN-LIKE FOLD / FERREDOXIN-LIKE FOLD / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


FAD binding / oxidoreductase activity
Similarity search - Function
Alpha-Beta Plaits - #2190 / Alpha-Beta Plaits - #2740 / : / Vanillyl-alcohol Oxidase; Chain A, domain 4 / Vanillyl-alcohol Oxidase; Chain A, domain 4 / FAD-linked oxidase, C-terminal / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / FAD-linked oxidase-like, C-terminal / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 ...Alpha-Beta Plaits - #2190 / Alpha-Beta Plaits - #2740 / : / Vanillyl-alcohol Oxidase; Chain A, domain 4 / Vanillyl-alcohol Oxidase; Chain A, domain 4 / FAD-linked oxidase, C-terminal / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / FAD-linked oxidase-like, C-terminal / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / PHOSPHATE ION / Unknown ligand / Oxidoreductase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.57 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Putative dehydrogenase (RPA1076) from Rhodopseudomonas palustris CGA009 at 2.57 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Feb 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)313,79236
Polymers307,3696
Non-polymers6,42330
Water16,556919
1
A: Putative oxidoreductase
B: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,59712
Polymers102,4562
Non-polymers2,14110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11230 Å2
ΔGint-95 kcal/mol
Surface area32100 Å2
MethodPISA
2
C: Putative oxidoreductase
D: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,59712
Polymers102,4562
Non-polymers2,14110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11320 Å2
ΔGint-96 kcal/mol
Surface area32080 Å2
MethodPISA
3
E: Putative oxidoreductase
F: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,59712
Polymers102,4562
Non-polymers2,14110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11370 Å2
ΔGint-95 kcal/mol
Surface area31900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.085, 250.728, 251.711
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A11 - 477
2114B11 - 477
3114C11 - 477
4114D11 - 477
5114E11 - 477
6114F11 - 477
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein
Putative oxidoreductase / Putative dehydrogenase


Mass: 51228.184 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Gene: RPA1076 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q6NAV4
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 6 / Source method: obtained synthetically
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 919 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 3.75 Å3/Da / Density % sol: 67.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.60M potassium dihydrogen phosphate, 25.00% Glycerol, 0.60M sodium dihydrogen phosphate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97922,0.97894
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 10, 2010
RadiationMonochromator: DOUBLE CRYSTAL SI (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979221
30.978941
ReflectionResolution: 2.57→49.357 Å / Num. obs: 144716 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 52.656 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 10.26
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.57-2.660.8241.75371214230199.9
2.66-2.770.67925633714940199.8
2.77-2.890.4782.95217713806199.9
2.89-3.050.34745756915236199.6
3.05-3.240.2435.65446614394199.6
3.24-3.480.158.75276413946199.2
3.48-3.830.10112.35517414562199.1
3.83-4.380.064185480514442198.5
4.38-5.50.04921.75500214442197.8
5.5-49.3570.03925.55596314800196

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
REFMAC5.5.0110refinement
XSCALEdata scaling
PDB_EXTRACT3.1data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.57→49.357 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 15.762 / SU ML: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.346 / ESU R Free: 0.24
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.A FLAVIN-ADENINE DINUCLEOTIDE (FAD) COFACTOR WAS MODELED INTO EACH OF THE SIX MONOMERS IN THE ASYMMETRIC UNIT. 6.AN UNKNOWN LIGAND (UNL) WAS MODELED INTO THE PUTATIVE ACTIVE NEAR THE FAD BINDING SITE ON EACH MONOMER 6. PHOSPHATE (PO4) AND POTASSIUM (K) FROM THE CRYSTALLIZATION WERE MODELED INTO THE STRUCTURE. THE OCCUPANCY ON SOME OF THE PHOSPHATES WERE DECREASED TO 0.5 TO ACCOUNT FOR THE DECREASED SCATTERING. 7. UNIDENTIFIED ELECTRON DENSITY NEAR ARG 56, ARG 103,AND HIS 128 ON EACH MONOMER WAS NOT MODELED. 8. THE ELECTRON DENSITIES CORRESPONDING TO ASN 45 ON THE B AND E CHAINS ARE POOR, AND THESE RESIDUES ARE RAMACHANDRAN OUTLIERS IN MOLPROBITY. GLN 146 ON THE F CHAIN CHAIN AND PRO 384 ON THE D AND E CHAINS ARE RAMACHANDRAN OUTLIERS IN MOLPROBITY EVEN THOUGH THEIR MODELING IS SUPPORTED BY ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2266 7270 5 %RANDOM
Rwork0.1931 ---
obs0.1948 144702 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 78.2 Å2 / Biso mean: 39.0054 Å2 / Biso min: 12.93 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å20 Å20 Å2
2---0.79 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.57→49.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20838 0 444 919 22201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02221795
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214309
X-RAY DIFFRACTIONr_angle_refined_deg1.299229753
X-RAY DIFFRACTIONr_angle_other_deg0.88335193
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.76152840
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.6624.673886
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.123153546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.34415137
X-RAY DIFFRACTIONr_chiral_restr0.0710.23469
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02124337
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024014
X-RAY DIFFRACTIONr_mcbond_it0.4451.513926
X-RAY DIFFRACTIONr_mcbond_other0.0581.55710
X-RAY DIFFRACTIONr_mcangle_it0.865222367
X-RAY DIFFRACTIONr_scbond_it1.11837869
X-RAY DIFFRACTIONr_scangle_it2.0094.57357
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 5793 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
AMEDIUM POSITIONAL0.220.5
BMEDIUM POSITIONAL0.190.5
CMEDIUM POSITIONAL0.190.5
DMEDIUM POSITIONAL0.230.5
EMEDIUM POSITIONAL0.230.5
FMEDIUM POSITIONAL0.240.5
AMEDIUM THERMAL0.222
BMEDIUM THERMAL0.192
CMEDIUM THERMAL0.192
DMEDIUM THERMAL0.192
EMEDIUM THERMAL0.22
FMEDIUM THERMAL0.22
LS refinement shellResolution: 2.57→2.637 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 535 -
Rwork0.317 10210 -
all-10745 -
obs--99.83 %
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)
10.04340.0536-0.01830.3873-0.17760.203-0.00810.0454-0.01410.03440.0637-0.1134-0.0252-0.0131-0.05560.03720.01-0.02650.0729-0.04210.083432.0832135.668131.0685
20.18670.17570.08230.41960.01690.1062-0.02420.0431-0.01490.1490.07490.0279-0.0437-0.0173-0.05070.12950.03960.01230.06510.00710.01679.8483156.466244.1229
30.2245-0.32530.04940.4395-0.06180.0450.042-0.02370.0119-0.15070.0011-0.0683-0.03570.0436-0.04310.1635-0.02560.01360.0895-0.01850.055563.7432156.397385.4639
4-0.0167-0.02360.03180.49690.25360.33070.0025-0.0402-0.0348-0.02850.03170.1469-0.0325-0.0022-0.03430.05520.0052-0.04130.09640.01040.118640.9819136.105898.4577
50.2006-0.17490.07130.4972-0.16380.0485-0.05820.02630.0268-0.09260.0396-0.07880.009-0.03660.01860.0706-0.0230.03380.085-0.01110.058641.364177.41-11.7751
60.25730.2711-0.08650.4419-0.22940.1102-0.0497-0.01270.03510.12770.0351-0.0773-0.0657-0.04790.01460.10340.0373-0.06010.0847-0.03010.098442.1218197.791614.1828
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 476
2X-RAY DIFFRACTION2B11 - 476
3X-RAY DIFFRACTION3C11 - 476
4X-RAY DIFFRACTION4D11 - 476
5X-RAY DIFFRACTION5E11 - 476
6X-RAY DIFFRACTION6F11 - 476

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