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- PDB-3c1a: Crystal structure of a putative oxidoreductase (ZP_00056571.1) fr... -

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Basic information

Entry
Database: PDB / ID: 3c1a
TitleCrystal structure of a putative oxidoreductase (ZP_00056571.1) from Magnetospirillum magnetotacticum MS-1 at 1.85 A resolution
ComponentsPutative oxidoreductase
KeywordsOXIDOREDUCTASE / ZP_00056571.1 / A Putative Oxidoreductase / Oxidoreductase family / NAD-binding Rossmann fold / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Putative oxidoreductase
Similarity search - Component
Biological speciesMagnetospirillum magnetotacticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative oxidoreductase (ZP_00056571.1) from Magnetospirillum magnetotacticum MS-1 at 1.85 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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 1.3Feb 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3105
Polymers66,8602
Non-polymers4513
Water11,602644
1
A: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7303
Polymers33,4301
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5802
Polymers33,4301
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.658, 86.361, 87.907
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-553-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: SER / End label comp-ID: SER / Refine code: 4 / Auth seq-ID: 8 - 314 / Label seq-ID: 9 - 315

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Putative oxidoreductase /


Mass: 33429.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum magnetotacticum (bacteria)
Strain: MS-1 / Gene: ZP_00056571.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: D0VWS9*PLUS
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#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-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 644 / Source method: isolated from a natural source / Formula: H2O
Sequence details1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED ...1. 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. 2. THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. THE SEQUENCE INFORMATION IS AVAILABLE AT GENBANK WITH ACCESSION CODE ZP_00056571.1 AND IN THE UNIPROT ARCHIVE (UNIPARC) WITH ACCESSION CODE UPI0000384B0A.

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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: 2.69 Å3/Da / Density % sol: 54.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: NANODROP, 19.6% PEG 3350, 0.15M Di-ammonium tartrate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.91840, 0.97953, 0.97939
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 26, 2007 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91841
20.979531
30.979391
ReflectionResolution: 1.85→29.988 Å / Num. obs: 61976 / % possible obs: 99.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 16.379 Å2 / Rmerge(I) obs: 0.145 / Rsym value: 0.145 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.85-1.93.50.88521584644920.88598.5
1.9-1.953.50.6642.41534043260.66498.8
1.95-2.013.50.592.81518242830.5999.4
2.01-2.073.60.4613.31491841760.46199.4
2.07-2.143.60.37841455640430.37899.6
2.14-2.213.60.3274.41424539260.32799.9
2.21-2.293.70.275.11387937970.27100
2.29-2.393.70.2525.51346536680.252100
2.39-2.493.70.226.11294735200.22100
2.49-2.623.70.17771242433790.177100
2.62-2.763.70.1581172131880.15100
2.76-2.933.70.1279.11123630620.127100
2.93-3.133.70.11110.51044028600.111100
3.13-3.383.60.09113983127010.091100
3.38-3.73.60.07815.5891424630.078100
3.7-4.143.60.06617.8815322500.066100
4.14-4.783.60.0620722620060.06100
4.78-5.853.60.05819.3613317190.058100
5.85-8.273.50.05618.9465713400.05699.9
8.27-29.9883.20.05423.425167770.05497.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→29.988 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.809 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.144
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN 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 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. PEG 3350 FRAGMENTS (PEG, PGE AND PG4) FROM CRYSTALLIZATION SOLUTION ARE MODELED. 5. RAMACHANDRAN OUTLIER OF RESIDUE PRO 259 IN THE B-SUBUNIT IS LOCATED IN POOR DENSITY. 6. ELECTRON DENSITY ALONG THE CRYSTALLOGRAPHIC TWO-FOLD AXIS NEAR THE SIDECHAIN OF THR B249 IS DISORDERED AND PRECLUDED THE RELIABLE MODELING OF THIS SIDECHAIN.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 3136 5.1 %RANDOM
Rwork0.214 ---
obs0.216 61925 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.499 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å20 Å20 Å2
2--2.3 Å20 Å2
3----1.28 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4476 0 30 644 5150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224733
X-RAY DIFFRACTIONr_bond_other_d0.0010.023108
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.9756491
X-RAY DIFFRACTIONr_angle_other_deg0.9637633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0175640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.98423.742163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61915697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4261530
X-RAY DIFFRACTIONr_chiral_restr0.0910.2755
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025383
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02875
X-RAY DIFFRACTIONr_nbd_refined0.2160.2959
X-RAY DIFFRACTIONr_nbd_other0.1980.23288
X-RAY DIFFRACTIONr_nbtor_refined0.170.22254
X-RAY DIFFRACTIONr_nbtor_other0.0890.22425
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2509
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0810.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2660.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.238
X-RAY DIFFRACTIONr_mcbond_it2.0633228
X-RAY DIFFRACTIONr_mcbond_other0.62631268
X-RAY DIFFRACTIONr_mcangle_it2.89555066
X-RAY DIFFRACTIONr_scbond_it4.8781715
X-RAY DIFFRACTIONr_scangle_it6.828111425
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3673 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.210.5
MEDIUM THERMAL0.822
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 240 -
Rwork0.299 4225 -
all-4465 -
obs--98.05 %

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