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- PDB-2oc5: Crystal structure of a ferritin-like protein (pmt1231) from proch... -

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Basic information

Entry
Database: PDB / ID: 2oc5
TitleCrystal structure of a ferritin-like protein (pmt1231) from prochlorococcus marinus str. mit 9313 at 1.68 A resolution
ComponentsHypothetical protein
KeywordsMETAL BINDING PROTEIN / Duf3066 family protein / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


aldehyde oxygenase (deformylating) activity / aldehyde oxygenase (deformylating) / transition metal ion binding
Similarity search - Function
Long-chain fatty aldehyde decarbonylase / Long-chain fatty aldehyde decarbonylase / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / : / Unknown ligand / Aldehyde decarbonylase
Similarity search - Component
Biological speciesProchlorococcus marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.68 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (NP_895059.1) from Prochlorococcus marinus MIT9313 at 1.68 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 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 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 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 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE 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.
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...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). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8115
Polymers27,6401
Non-polymers1714
Water5,585310
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.350, 77.350, 116.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-359-

HOH

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Components

#1: Protein Hypothetical protein


Mass: 27640.135 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prochlorococcus marinus (bacteria) / Strain: MIT 9313 / Gene: NP_895059.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7V6D4
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O
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: 3.16 Å3/Da / Density % sol: 61.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.8
Details: 0.2M KAcetate, 20.0% PEG-3350, No Buffer pH 7.8, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162, 0.97929, 0.97915
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 5, 2006 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979291
30.979151
ReflectionResolution: 1.68→29.235 Å / Num. obs: 41123 / % possible obs: 99.6 % / Biso Wilson estimate: 30.354 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 10.19
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
1.68-1.740.5452.0825789702897.2
1.74-1.810.432.827749740995.2
1.81-1.890.3523.727227724995.9
1.89-1.990.2555.228407757797.3
1.99-2.120.1637.729877793299
2.12-2.280.1081128514755799.4
2.28-2.510.08713.329205772999.6
2.51-2.870.0741628736763799.7
2.870.05719.228948771999.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SOLVEphasing
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.68→29.235 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.906 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.08
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE 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 THE 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.TWO FE ATOMS AND AN UNKNOWN LIGAND (UNL) WERE MODELED INTO ELECTRON DENISTY NEAR GLU 45, GLU 73, HIS 76 GLU 128, AND HIS 160. AN ACETATE MOLECULE FROM THE CRYSTALLIZATION WAS ALSO MODELED. THE PRESENCE OF THE TWO IRON ATOMS IS SUPPORTED BY X-RAY FLUORESCENCE MEASUREMENTS, ANOMALOUS DIFFERENCE FOURIERS AND GEOMETRY. 5.RESIDUES 1-19 AT N-TERMINAL END ARE DISORDERED AND NOT BUILT IN THIS MODEL. 6.UNEXPLAINED ELECTRON DENSITY IS LOCATED NEAR ALA 238 AND ALA 239.
RfactorNum. reflection% reflectionSelection details
Rfree0.2 2060 5 %RANDOM
Rwork0.164 ---
obs0.166 40994 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.126 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.68→29.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 0 26 310 2072
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221885
X-RAY DIFFRACTIONr_bond_other_d0.0020.021763
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.9712555
X-RAY DIFFRACTIONr_angle_other_deg0.89334082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5845241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75123.65693
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.29315326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4081517
X-RAY DIFFRACTIONr_chiral_restr0.0910.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022136
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02396
X-RAY DIFFRACTIONr_nbd_refined0.240.3490
X-RAY DIFFRACTIONr_nbd_other0.1750.31745
X-RAY DIFFRACTIONr_nbtor_refined0.1820.5941
X-RAY DIFFRACTIONr_nbtor_other0.0830.51040
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.5356
X-RAY DIFFRACTIONr_metal_ion_refined0.020.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.34
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3630.328
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.533
X-RAY DIFFRACTIONr_mcbond_it2.0331180
X-RAY DIFFRACTIONr_mcbond_other0.5613466
X-RAY DIFFRACTIONr_mcangle_it2.73451857
X-RAY DIFFRACTIONr_scbond_it4.798774
X-RAY DIFFRACTIONr_scangle_it6.36611693
LS refinement shellResolution: 1.679→1.723 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 126 -
Rwork0.23 2728 -
obs-2854 95.01 %
Refinement TLS params.Method: refined / Origin x: 18.199 Å / Origin y: 36.904 Å / Origin z: 39.066 Å
111213212223313233
T-0.0138 Å20.0096 Å20.0175 Å2--0.041 Å20.0235 Å2---0.0397 Å2
L0.518 °20.1766 °20.0753 °2-0.9745 °2-0.0594 °2--0.5853 °2
S0.0076 Å °-0.0064 Å °0.0194 Å °-0.0078 Å °-0.0196 Å °0.0205 Å °0.0106 Å °0.0077 Å °0.012 Å °
Refinement TLS groupSelection: ALL

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