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- PDB-2nvn: Crystal structure of a protein with a cupin-like fold and unknown... -

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Basic information

Entry
Database: PDB / ID: 2nvn
TitleCrystal structure of a protein with a cupin-like fold and unknown function (YP_400729.1) from Synechococcus SP. PCC 7942 (Elongatus) at 2.50 A resolution
ComponentsHypothetical protein
KeywordsStructural Genomics/Unknown function / YP_400729.1 / hypothetical protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG / Structural Genomics-Unknown function COMPLEX
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Protein of unknown function DUF1818 / Domain of unknown function (DUF1818) / Transcriptional Coactivator Pc4; Chain A / ssDNA-binding transcriptional regulator / Transcriptional Co-activator pc4; Chain A / Roll / Mainly Beta
Similarity search - Domain/homology
DUF1818 domain-containing protein / Uncharacterized protein
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (YP_400729.1) from Synechococcus SP. PCC 7942 (Elongatus) at 2.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: 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 / 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
Revision 1.5Nov 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 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). ASSIGNMENT OF BIOMOLECULE AS A DIMER IS BASED UPON EBI/PISA ANALYSIS.

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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)13,6242
Polymers13,5321
Non-polymers921
Water66737
1
A: Hypothetical protein
hetero molecules

A: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2484
Polymers27,0642
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)82.180, 82.180, 80.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Hypothetical protein


Mass: 13531.932 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: PCC 7942 / Gene: YP_400729.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5MZF1, UniProt: Q31MH7*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 5.02 Å3/Da / Density % sol: 75.5 %
Crystal growTemperature: 277 K / pH: 8
Details: 2.5M NaCl, 0.1M Imidazole, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9805
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 9, 2006 / Details: FIXED-HEIGHT EXIT BEAM, TOROIDAL FOCUSING MIRROR
RadiationMonochromator: DOUBLE-CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9805 Å / Relative weight: 1
ReflectionResolution: 2.5→29.05 Å / Num. obs: 10011 / % possible obs: 99.4 % / Redundancy: 6.88 % / Biso Wilson estimate: 71.4 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 13.56
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.797 / Mean I/σ(I) obs: 1.63 / % possible all: 97.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→29.05 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.948 / SU B: 15.45 / SU ML: 0.166 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.223 / ESU R Free: 0.186
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 RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.227 478 4.8 %RANDOM
Rwork0.208 ---
obs0.209 9972 99.8 %-
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: 26.66 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å20 Å20 Å2
2---1.14 Å20 Å2
3---2.28 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms930 0 6 37 973
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022971
X-RAY DIFFRACTIONr_bond_other_d0.0030.02649
X-RAY DIFFRACTIONr_angle_refined_deg1.8231.9621326
X-RAY DIFFRACTIONr_angle_other_deg1.47931568
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1265124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.16922.95544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.18915151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3811510
X-RAY DIFFRACTIONr_chiral_restr0.1080.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021098
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02207
X-RAY DIFFRACTIONr_nbd_refined0.1810.2152
X-RAY DIFFRACTIONr_nbd_other0.1460.2583
X-RAY DIFFRACTIONr_nbtor_refined0.1620.2427
X-RAY DIFFRACTIONr_nbtor_other0.0790.2532
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.228
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0980.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2160.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0810.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8631.5703
X-RAY DIFFRACTIONr_mcbond_other0.1361.5246
X-RAY DIFFRACTIONr_mcangle_it1.1312964
X-RAY DIFFRACTIONr_scbond_it1.7483413
X-RAY DIFFRACTIONr_scangle_it2.6534.5360
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.435 31 -
Rwork0.381 709 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 13.618 Å / Origin y: 23.488 Å / Origin z: 29.814 Å
111213212223313233
T0.3425 Å2-0.0992 Å2-0.0374 Å2-0.3513 Å20.0163 Å2--0.0305 Å2
L3.6133 °2-1.112 °22.1403 °2-5.6788 °2-3.1778 °2--5.5905 °2
S0.2312 Å °0.1975 Å °-0.2486 Å °-0.6194 Å °0.1222 Å °0.386 Å °0.2356 Å °-0.3572 Å °-0.3534 Å °

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