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- PDB-2okf: CRYSTAL STRUCTURE OF A FDXN ELEMENT EXCISION CONTROLLING FACTOR P... -

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Basic information

Entry
Database: PDB / ID: 2okf
TitleCRYSTAL STRUCTURE OF A FDXN ELEMENT EXCISION CONTROLLING FACTOR PROTEIN (AVA_3312) FROM ANABAENA VARIABILIS AT 1.60 A RESOLUTION
ComponentsFdxN element excision controlling factor protein
KeywordsDNA BINDING PROTEIN / XISH PROTEIN / FDXN ELEMENT EXCISION CONTROLLING FACTOR PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


nuclease activity / nucleic acid binding
Similarity search - Function
XisH protein / XisH protein / Trna Endonuclease; Chain: A, domain 1 - #10 / Trna Endonuclease; Chain: A, domain 1 / tRNA endonuclease-like domain superfamily / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FdxN element excision controlling factor protein
Similarity search - Component
Biological speciesAnabaena variabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2014
Title: Site-specific recombination of nitrogen-fixation genes in cyanobacteria by XisF-XisH-XisI complex: Structures and models.
Authors: Hwang, W.C. / Golden, J.W. / Pascual, J. / Xu, D. / Cheltsov, A. / Godzik, A.
History
DepositionJan 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Sep 10, 2014Group: Database references
Revision 1.4Sep 24, 2014Group: Database references
Revision 1.5Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.6Jan 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
Remark 999 SEQUENCE 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FdxN element excision controlling factor protein
B: FdxN element excision controlling factor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,71615
Polymers31,9682
Non-polymers74813
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-17 kcal/mol
Surface area12340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.810, 59.810, 73.190
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ARG / End label comp-ID: ASN / Refine code: 1 / Auth seq-ID: 4 - 139 / Label seq-ID: 5 - 140

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein FdxN element excision controlling factor protein


Mass: 15984.097 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena variabilis (bacteria) / Strain: PCC 7937 / Gene: YP_323815.1, Ava_3312 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q3M7W6
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: NANODROP, 0.2M (NH4)2SO4, 25.0% PEG 4000, 0.1M Acetate pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91162, 0.97937, 0.97905
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
10.911621
20.979371
30.979051
ReflectionResolution: 1.6→25.898 Å / Num. obs: 38600 / % possible obs: 96.3 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 12.07
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
1.6-1.660.2423.213902722488.7
1.66-1.720.1953.912649653993.6
1.72-1.80.1515.114506750894.3
1.8-1.90.1096.915084781596.1
1.9-2.020.0789.514613756597.1
2.02-2.170.05811.914155732898.1
2.17-2.390.04315.514928773398.7
2.39-2.730.04317.314507757198.8
2.730.03320.914794771999.3

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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: 1.6→25.898 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.185 / SU ML: 0.04 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.066
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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. TWO CHLORIDE IONS, TWO ACETATE IONS, AND NINE ETHYLENE GLYCOL MOLECULES WERE MODELED BASED ON CRYSTALLIZATION CONDITIONS. 5. RESIDUES 1-3 AND 37-43 FROM BOTH CHAINS ARE DISORDERED AND WERE NOT BUILT IN THIS MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.155 1937 5 %RANDOM
Rwork0.142 ---
all0.143 ---
obs0.143 38571 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.211 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.6→25.898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2063 0 46 285 2394
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222260
X-RAY DIFFRACTIONr_bond_other_d0.0010.022134
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.9613073
X-RAY DIFFRACTIONr_angle_other_deg0.86634971
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8035289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81525.514107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.72415406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.322158
X-RAY DIFFRACTIONr_chiral_restr0.1010.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022483
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02437
X-RAY DIFFRACTIONr_nbd_refined0.2240.3446
X-RAY DIFFRACTIONr_nbd_other0.1760.32222
X-RAY DIFFRACTIONr_nbtor_refined0.1890.51115
X-RAY DIFFRACTIONr_nbtor_other0.0860.51293
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2250.5372
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.323
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.364
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.542
X-RAY DIFFRACTIONr_mcbond_it2.08231445
X-RAY DIFFRACTIONr_mcbond_other0.4213543
X-RAY DIFFRACTIONr_mcangle_it2.69452208
X-RAY DIFFRACTIONr_scbond_it4.1468988
X-RAY DIFFRACTIONr_scangle_it5.48211848
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2036 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
TIGHT POSITIONAL0.040.05
TIGHT THERMAL0.130.5
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.196 139 -
Rwork0.161 2650 -
obs-2789 97.52 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9026-0.8036-0.84990.80110.1870.80630.04210.02490.1124-0.03110.011-0.1068-0.1060.0863-0.0532-0.1435-0.01280.0171-0.0772-0.0141-0.10570.85814.83817.762
21.7852-0.8877-0.65340.95770.64230.92820.0269-0.04650.15520.01230.03-0.0526-0.13110.0574-0.0569-0.08790.01960.0184-0.1404-0.0091-0.1069-17.47825.46634.558
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 4 - 139 / Label seq-ID: 5 - 140

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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