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- PDB-1np7: Crystal Structure Analysis of Synechocystis sp. PCC6803 cryptochrome -

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Basic information

Entry
Database: PDB / ID: 1np7
TitleCrystal Structure Analysis of Synechocystis sp. PCC6803 cryptochrome
ComponentsDNA photolyase
KeywordsLYASE / protein with FAD cofactor
Function / homology
Function and homology information


DNA photolyase activity / photoreactive repair / : / FAD binding / DNA binding
Similarity search - Function
Cryptochrome DASH / Cryptochrome/DNA photolyase class 1, conserved site, C-terminal / DNA photolyases class 1 signature 1. / DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain / FAD binding domain of DNA photolyase / DNA photolyase, N-terminal ...Cryptochrome DASH / Cryptochrome/DNA photolyase class 1, conserved site, C-terminal / DNA photolyases class 1 signature 1. / DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain / FAD binding domain of DNA photolyase / DNA photolyase, N-terminal / Cryptochrome/photolyase, N-terminal domain superfamily / DNA photolyase / Photolyase/cryptochrome alpha/beta domain profile. / Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Cryptochrome DASH
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBrudler, R. / Hitomi, K. / Daiyasu, H. / Toh, H. / Kucho, K. / Ishiura, M. / Kanehisa, M. / Roberts, V.A. / Todo, T. / Tainer, J.A. / Getzoff, E.D.
CitationJournal: Mol.Cell / Year: 2003
Title: Identification of a new cryptochrome class: structure, function, and evolution
Authors: Brudler, R. / Hitomi, K. / Daiyasu, H. / Toh, H. / Kucho, K. / Ishiura, M. / Kanehisa, M. / Roberts, V.A. / Todo, T. / Tainer, J.A. / Getzoff, E.D.
History
DepositionJan 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE Residues 1-37 are not cloning artifacts and belong to the protein structure. The ...SEQUENCE Residues 1-37 are not cloning artifacts and belong to the protein structure. The discrepancy arises because the entry S74805 in GenBank is missing the first N-terminal 37 residues.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA photolyase
B: DNA photolyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,0837
Polymers114,2242
Non-polymers1,8595
Water6,269348
1
A: DNA photolyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0894
Polymers57,1121
Non-polymers9783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA photolyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9933
Polymers57,1121
Non-polymers8822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.284, 89.477, 121.687
Angle α, β, γ (deg.)90.00, 120.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DNA photolyase


Mass: 57111.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Plasmid: pGEX 4T-2, PCC6803 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P77967
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Crystal grow
*PLUS
Temperature: 20-24 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115 mg/mlprotein1drop
250 mMTris1drop
350 mM1dropNaCl
41 Mdithiothreitol1drop
510 %glycerol1droppH8.0
655 %satammonium sulfate1reservoir
70.1 MMES1reservoirpH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 3, 2000
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 88628 / Num. obs: 88628 / % possible obs: 96.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 16.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 8731 / Rsym value: 0.311 / % possible all: 95.8
Reflection
*PLUS
Lowest resolution: 30 Å
Reflection shell
*PLUS
% possible obs: 95.8 % / Rmerge(I) obs: 0.311

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DNP

1dnp


Resolution: 1.9→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.233 4299 RANDOM
Rwork0.208 --
all0.209 85033 -
obs0.209 85033 -
Displacement parametersBiso mean: 24 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7998 0 121 348 8467
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.219
LS refinement shellResolution: 1.9→1.91 Å
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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