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- PDB-2od5: CRYSTAL STRUCTURE OF A PUTATIVE NUCLEIC ACID BINDING PROTEIN (JCV... -

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Basic information

Entry
Database: PDB / ID: 2od5
TitleCRYSTAL STRUCTURE OF A PUTATIVE NUCLEIC ACID BINDING PROTEIN (JCVI_PEP_1096688149193) FROM UNCULTURED MARINE ORGANISM AT 1.79 A RESOLUTION
Componentshypothetical protein
KeywordsDNA BINDING PROTEIN / METAGENOMICS / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyWinged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / IMIDAZOLE
Function and homology information
Biological speciesuncultured marine organism (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.79 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (JCVI_PEP_1096688149193) from an environmental metagenome (unidentified marine microbe), Sorcerer II Global Ocean Sampling experiment at 1.79 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 21, 2006Deposition 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 / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAINS. ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAINS. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). ASSINMENT OF A TETRAMER AS BIOMOLECULE IS SUPPORTED BY EBI/PISA ANALYSIS. HOWEVER, SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
Remark 999SEQUENCE (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 SEQUENCE OF THE PROTEIN WAS NOT AVAILABLE IN THE UNP DATABASE AT THE TIME OF PROCESSING. (3) PRODUCT OF THE EXPRESSED SYNTHETIC GENE WAS BASED ON THE PREDICTED SEQUENCE OF ACCESSION ID JCVI_PEP_1096688149193 FROM THE J. CRAIG VENTER INSTITUTE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9538
Polymers13,1851
Non-polymers7677
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: hypothetical protein
hetero molecules

A: hypothetical protein
hetero molecules

A: hypothetical protein
hetero molecules

A: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,81132
Polymers52,7424
Non-polymers3,06928
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area10650 Å2
ΔGint-56 kcal/mol
Surface area20080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)64.406, 64.406, 133.246
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
DetailsASSINMENT OF A TETRAMER AS BIOMOLECULE IS SUPPORTED BY EBI/PISA ANALYSIS. HOWEVER, SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein hypothetical protein


Mass: 13185.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured marine organism (environmental samples)
Description: SYNTHETIC GENE: The gene product was based on JCVI_PEP_1096688149193 from the Sorcerer II Global Ocean Sampling experiment
Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 84 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 3.02 Å3/Da / Density % sol: 59.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7
Details: 1.0M LiCl, 20.0% PEG-6000, 0.1M HEPES pH 7.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97971
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 19, 2006 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979711
ReflectionResolution: 1.6→28.989 Å / Num. obs: 16175 / % possible obs: 100 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.137 / Rsym value: 0.137 / Net I/σ(I): 3.9
Reflection shell

Rmerge(I) obs: 0.017 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.79-1.84140.41614011541.674100
1.84-1.8913.90.61569111251.244100
1.89-1.9413.90.71544711081.042100
1.94-213.91.11505410820.669100
2-2.07141.41441410330.498100
2.07-2.141421424510210.379100
2.14-2.2213.92.2134729700.337100
2.22-2.3113.82.5130649450.302100
2.31-2.4113.93.3124939020.228100
2.41-2.5313.73.8120248760.194100
2.53-2.6713.74.5114838360.163100
2.67-2.8313.75106917810.139100
2.83-3.0313.55.6101957550.121100
3.03-3.2713.46.694937110.099100
3.27-3.5813.36.986646520.088100
3.58-413.17.179276040.077100
4-4.6212.8869115380.073100
4.62-5.6612.68.358224630.069100
5.66-8.0111.97.845643840.071100
8.01-28.999.89.923142350.05797.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SOLVEphasing
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.79→28.989 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.899 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.093
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. 4. EDO MOLECULES FROM THE CRYO SOLUTION ARE MODELED. 5. PEG6000 FRAGMENTS (1PE) FROM CRYSTALLIZATION SOLUTION ARE MODELED. 6. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 809 5 %RANDOM
Rwork0.189 ---
obs0.19 16127 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.725 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.79→28.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms720 0 45 77 842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021812
X-RAY DIFFRACTIONr_bond_other_d0.0020.02599
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.9671088
X-RAY DIFFRACTIONr_angle_other_deg0.95431450
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6645103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39422.94134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59515145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.303157
X-RAY DIFFRACTIONr_chiral_restr0.0930.2118
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02868
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02166
X-RAY DIFFRACTIONr_nbd_refined0.2270.2196
X-RAY DIFFRACTIONr_nbd_other0.1980.2597
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2385
X-RAY DIFFRACTIONr_nbtor_other0.0870.2454
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.240
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3090.2111
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.216
X-RAY DIFFRACTIONr_mcbond_it2.3783508
X-RAY DIFFRACTIONr_mcbond_other0.5293193
X-RAY DIFFRACTIONr_mcangle_it3.4375770
X-RAY DIFFRACTIONr_scbond_it5.2538378
X-RAY DIFFRACTIONr_scangle_it6.74311311
LS refinement shellResolution: 1.79→1.836 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 60 -
Rwork0.258 1089 -
obs-1149 99.91 %
Refinement TLS params.Method: refined / Origin x: 17.543 Å / Origin y: 5.431 Å / Origin z: 10.004 Å
111213212223313233
T-0.1171 Å2-0.0077 Å20.0178 Å2--0.0171 Å2-0.0486 Å2---0.1759 Å2
L1.1175 °2-0.4615 °20.5187 °2-0.8977 °2-0.2738 °2--2.2854 °2
S-0.0145 Å °-0.0371 Å °0.026 Å °0.0734 Å °0.0376 Å °0.067 Å °-0.1185 Å °0.1575 Å °-0.0231 Å °
Refinement TLS groupSelection: ALL

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