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- PDB-2osd: Crystal structure of a vinyl-4-reductase family protein (mj_1460)... -

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Basic information

Entry
Database: PDB / ID: 2osd
TitleCrystal structure of a vinyl-4-reductase family protein (mj_1460) from methanocaldococcus jannaschii dsm at 2.40 A resolution
ComponentsHypothetical protein MJ1460
KeywordsMETAL BINDING PROTEIN / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


4-vinyl reductase, 4VR / V4R domain / V4R / Trafficking protein particle complex subunit 3 / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / NO signalling/Golgi transport ligand-binding domain superfamily / N-6 Adenine-specific DNA methylases signature. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein MJ1460
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein MJ_1460 (1592102) from Methanococcus jannaschii at 2.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Jan 25, 2023Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.6Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999 SEQUENCE 1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE 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 CONSTRUCT WAS ENGINEERED WITH THE FOLLOWING MUTATIONS: K132Y, K133Y AND K134Y

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein MJ1460
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5698
Polymers19,2021
Non-polymers3677
Water54030
1
A: Hypothetical protein MJ1460
hetero molecules

A: Hypothetical protein MJ1460
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,13816
Polymers38,4032
Non-polymers73414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area7460 Å2
ΔGint-105 kcal/mol
Surface area13200 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)55.786, 55.786, 118.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Hypothetical protein MJ1460


Mass: 19201.564 Da / Num. of mol.: 1 / Fragment: V4R domain / Mutation: K132Y, K133Y, K134Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Species: Methanocaldococcus jannaschii / Strain: DSM 2661, JAL-1, JCM 10045, NBRC 100440 / Gene: 1592102, MJ1460 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q58855

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Non-polymers , 5 types, 37 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: NANODROP, 0.2M CaCl2, 20.0% PEG 3350, No Buffer, pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97879, 0.97908
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 7, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.978791
30.979081
ReflectionResolution: 2.3→29.748 Å / Num. obs: 8939 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.367.10.9170.845116360.917100
2.36-2.427.10.8290.945306390.829100
2.42-2.497.10.746141845910.746100
2.49-2.577.10.5781.341765910.578100
2.57-2.6670.4571.741605920.457100
2.66-2.7570.3772.138045400.377100
2.75-2.8570.2662.938175480.266100
2.85-2.977.10.23.836665200.2100
2.97-3.16.90.1495.134925030.149100
3.1-3.2570.123633364770.123100
3.25-3.436.90.16.931674590.1100
3.43-3.646.80.0798.429914370.079100
3.64-3.896.90.0689.628754190.068100
3.89-4.26.80.0581026833950.058100
4.2-4.66.70.0512.424013580.05100
4.6-5.146.60.04414.321753310.044100
5.14-5.946.40.05810.419463020.058100
5.94-7.276.30.06110.116232590.061100
7.27-10.295.90.03915.312492130.03999.6
10.29-29.754.90.03817.16351290.03894.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→29.748 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.951 / SU B: 15.426 / SU ML: 0.198 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.305 / ESU R Free: 0.217
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. RESIDUES 45-46 ARE DISORDERED AND NOT VISIBLE IN THE ELECTRON DENSITY MAPS. THEY WERE NOT MODELED. 5. TWO CA, THREE ETHYLENE GLYCOL MOLECULES, ONE CL ION FROM THE CRYSTALLIZATION BUFFER WERE MODELED INTO THE STRUCTURE. 6. A ZN ATOM OF THE SUBUNIT IN THE ASYMMETRIC UNIT IS COORDINATED TO THE SIDE CHAINS OF HIS 116, GLU 139, CYS 142 AND CYS 150. X-RAY FLUORESCENCE EXPERIMENTS SUPPORT THE ASSIGNMENT OF THE ZINC ION.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 421 4.7 %RANDOM
Rwork0.219 ---
all0.221 ---
obs0.221 8895 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å20 Å2
2--0.71 Å20 Å2
3----1.43 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1177 0 16 30 1223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221234
X-RAY DIFFRACTIONr_bond_other_d0.0020.02845
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.9841665
X-RAY DIFFRACTIONr_angle_other_deg0.96232078
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.225152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.61725.92654
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.23615211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg31.953151
X-RAY DIFFRACTIONr_chiral_restr0.0910.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021355
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02237
X-RAY DIFFRACTIONr_nbd_refined0.2260.2241
X-RAY DIFFRACTIONr_nbd_other0.1870.2777
X-RAY DIFFRACTIONr_nbtor_refined0.1930.2587
X-RAY DIFFRACTIONr_nbtor_other0.0930.2647
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.241
X-RAY DIFFRACTIONr_metal_ion_refined0.3230.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3750.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1830.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.24
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1370.22
X-RAY DIFFRACTIONr_mcbond_it2.2233790
X-RAY DIFFRACTIONr_mcbond_other0.4463302
X-RAY DIFFRACTIONr_mcangle_it3.52651232
X-RAY DIFFRACTIONr_scbond_it6.3688512
X-RAY DIFFRACTIONr_scangle_it7.96311432
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 29 -
Rwork0.281 603 -
obs-632 99.84 %
Refinement TLS params.Method: refined / Origin x: 12.696 Å / Origin y: 4.8495 Å / Origin z: 28.4007 Å
111213212223313233
T-0.1232 Å2-0.0169 Å2-0.0221 Å2--0.3418 Å2-0.044 Å2---0.2538 Å2
L3.7316 °20.0404 °20.1906 °2-4.8298 °21.3634 °2--5.029 °2
S-0.1126 Å °0.091 Å °0.3192 Å °-0.2104 Å °0.1143 Å °-0.1761 Å °-0.5322 Å °0.3015 Å °-0.0017 Å °
Refinement TLS groupSelection: ALL

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