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- PDB-2oh3: Crystal structure of COG1633: Uncharacterized conserved protein (... -

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Basic information

Entry
Database: PDB / ID: 2oh3
TitleCrystal structure of COG1633: Uncharacterized conserved protein (ZP_00055496.1) from Magnetospirillum magnetotacticum MS-1 at 2.00 A resolution
ComponentsCOG1633: Uncharacterized conserved protein
KeywordsMETAL BINDING PROTEIN / Rubrerythrin / ZP_00055496.1 / COG1633: Uncharacterized conserved protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


oxidoreductase activity / metal ion binding
Similarity search - Function
Rubrerythrin, diiron-binding domain / Rubrerythrin / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
IMIDAZOLE / TRIETHYLENE GLYCOL / Uncharacterized conserved protein
Similarity search - Component
Biological speciesMagnetospirillum magnetotacticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of COG1633: Uncharacterized conserved protein (ZP_00055496.1) from Magnetospirillum magnetotacticum MS-1 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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.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.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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). AUTHORS STATE THAT STATIC LIGHT SCATTERING WITH ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY MEASUREMENTS INDICATE THAT THE DIMER IS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION
Remark 999 SEQUENCE (1) THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. ... SEQUENCE (1) THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL 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 DATABASE AT THE TIME OF DEPOSITION. (3) THE SEQUENCE IS AVAILABLE FROM GENBANK UNDER ACCESSION ID ZP_00055496.1 AND FROM THE UNIPROT ARCHIVE UNDER ACCESSION ID UPI00003846C6

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COG1633: Uncharacterized conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9095
Polymers19,4751
Non-polymers4354
Water2,000111
1
A: COG1633: Uncharacterized conserved protein
hetero molecules

A: COG1633: Uncharacterized conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,81910
Polymers38,9492
Non-polymers8708
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)64.360, 75.280, 89.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein COG1633: Uncharacterized conserved protein / Rubrerythrin


Mass: 19474.623 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum magnetotacticum (bacteria)
Strain: MS-1 / Gene: ZP_00055496.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q2VZ87*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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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: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growTemperature: 277 K / pH: 7.1
Details: NANODROP, 0.2M NaF, 20.0% PEG-3350, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 7.10

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97913
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 18, 2006 / 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
20.979131
ReflectionResolution: 2→28.105 Å / Num. obs: 14778 / % possible obs: 96.8 % / Biso Wilson estimate: 37.83 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 16.21
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 2.16 / % possible all: 94.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→28.11 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.432 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.15
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 RESIDUAL B FACTORS ONLY. 4. THE RESIDUES 1-2, 85-87, AND 155-166 ARE DISORDERED AND WERE NOT BUILT DUE TO INSUFFICIENT ELECTRON DENSITY. 5. THE PRESENCE OF ZINC IS SUPPORTED WITH X-RAY FLOURESCENCE AND ANOMALOUS DIFFERENCE FOURIER MAPS. 6. IMIDAZOLE AND PEG WERE MODELED BASED ON CRYSTALLIZATION AND PURIFICATION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 744 5 %RANDOM
Rwork0.192 ---
obs0.195 14778 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.89 Å2
Baniso -1Baniso -2Baniso -3
1--2.24 Å20 Å20 Å2
2---0.27 Å20 Å2
3---2.52 Å2
Refinement stepCycle: LAST / Resolution: 2→28.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1178 0 26 111 1315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221274
X-RAY DIFFRACTIONr_bond_other_d0.0030.021137
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.9621727
X-RAY DIFFRACTIONr_angle_other_deg0.90932644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1565163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.19423.96863
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20115211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.839159
X-RAY DIFFRACTIONr_chiral_restr0.0830.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021428
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02264
X-RAY DIFFRACTIONr_nbd_refined0.2250.2290
X-RAY DIFFRACTIONr_nbd_other0.1930.21085
X-RAY DIFFRACTIONr_nbtor_refined0.1850.2601
X-RAY DIFFRACTIONr_nbtor_other0.0890.2720
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.276
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0920.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2830.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3440.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9041.5786
X-RAY DIFFRACTIONr_mcbond_other0.2361.5305
X-RAY DIFFRACTIONr_mcangle_it1.47921227
X-RAY DIFFRACTIONr_scbond_it2.4343555
X-RAY DIFFRACTIONr_scangle_it3.7854.5492
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 50 -
Rwork0.25 1005 -
obs--95.22 %
Refinement TLS params.Method: refined / Origin x: 31.0082 Å / Origin y: 24.553 Å / Origin z: 13.7822 Å
111213212223313233
T-0.1218 Å2-0.0219 Å2-0.0042 Å2--0.1607 Å20.0345 Å2---0.1768 Å2
L5.1804 °2-0.7722 °21.1 °2-1.7399 °2-0.3541 °2--1.628 °2
S-0.0297 Å °0.2462 Å °0.2082 Å °-0.132 Å °0.0244 Å °0.0003 Å °0.0029 Å °0.0489 Å °0.0053 Å °

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