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- PDB-3d7q: Crystal structure of a xisi-like protein (npun_ar114) from nostoc... -

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Basic information

Entry
Database: PDB / ID: 3d7q
TitleCrystal structure of a xisi-like protein (npun_ar114) from nostoc punctiforme pcc 73102 at 2.30 A resolution
ComponentsXisI protein-like
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyXisI-like / XisI protein / XisI-like superfamily / XisI protein / TATA-Binding Protein / 2-Layer Sandwich / Alpha Beta / FdxN element excision controlling factor protein
Function and homology information
Biological speciesNostoc punctiforme PCC 73102 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 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
DepositionMay 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 10, 2014Group: Database references
Revision 1.3Oct 14, 2015Group: Database references
Revision 1.4Dec 23, 2015Group: Database references
Revision 1.5Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.6Jul 24, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: software / struct_conn / struct_ref_seq
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 1.7Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: XisI protein-like
B: XisI protein-like


Theoretical massNumber of molelcules
Total (without water)26,9572
Polymers26,9572
Non-polymers00
Water99155
1
B: XisI protein-like

B: XisI protein-like


Theoretical massNumber of molelcules
Total (without water)26,9572
Polymers26,9572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area2050 Å2
ΔGint-8 kcal/mol
Surface area11570 Å2
MethodPISA
2
A: XisI protein-like

A: XisI protein-like


Theoretical massNumber of molelcules
Total (without water)26,9572
Polymers26,9572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area2090 Å2
ΔGint-6 kcal/mol
Surface area11030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.846, 79.846, 74.256
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 3

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPLEULEUAA2 - 193 - 20
21ASPASPLEULEUBB2 - 193 - 20
12GLYGLYGLUGLUAA26 - 11127 - 112
22GLYGLYGLUGLUBB26 - 11127 - 112

NCS ensembles :
ID
1
2

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Components

#1: Protein XisI protein-like


Mass: 13478.509 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme PCC 73102 (bacteria)
Gene: ZP_00106052.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: B2JAN5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.15M lithium sulfate, 26.0% polyethylene glycol 4000, 0.1M TRIS pH 9.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97937,0.97854
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 13, 2008 / 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
20.979371
30.978541
ReflectionResolution: 2.3→28.228 Å / Num. obs: 11187 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 46.112 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 6.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.367.20.766158008060.766100
2.36-2.427.20.6081.356727870.608100
2.42-2.497.20.5151.555057650.515100
2.49-2.577.20.4331.853227420.433100
2.57-2.667.20.3312.352637290.331100
2.66-2.757.20.2712.850016990.271100
2.75-2.857.20.2083.748336750.208100
2.85-2.977.20.1674.547316600.167100
2.97-3.17.20.1425.444206170.142100
3.1-3.257.10.1146.342866040.114100
3.25-3.437.10.0947.241145780.094100
3.43-3.6470.0768.739075550.076100
3.64-3.8970.05810.736005120.058100
3.89-4.270.05111.934394930.051100
4.2-4.66.90.04911.730444390.049100
4.6-5.146.80.04712.428474180.047100
5.14-5.946.70.05810.324603680.058100
5.94-7.276.40.0669.221013280.066100
7.27-10.296.20.04911.115872580.049100
10.29-28.235.20.04711.67941540.04795

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3.004data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→28.228 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.913 / SU B: 16.459 / SU ML: 0.194 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.388 / ESU R Free: 0.258
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 ...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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (3). ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. (4). RESIDUES SER23 AND TYR25 IN SUBUNIT A ARE LOCATED IN POOR DENSITY AND NOT MODELED. (5). UNEXPLAINED ELECTRON DENSITY NEAR RESIDUE 102 IN SUBUNIT B WAS NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.259 531 4.8 %RANDOM
Rwork0.206 ---
obs0.208 11148 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.396 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2--0.77 Å20 Å2
3----1.53 Å2
Refinement stepCycle: LAST / Resolution: 2.3→28.228 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1807 0 0 55 1862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211899
X-RAY DIFFRACTIONr_bond_other_d0.0080.021267
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.9342571
X-RAY DIFFRACTIONr_angle_other_deg1.0133111
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7355230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg47.08625.545101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.21615357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.645158
X-RAY DIFFRACTIONr_chiral_restr0.0960.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022130
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02358
X-RAY DIFFRACTIONr_nbd_refined0.1990.2319
X-RAY DIFFRACTIONr_nbd_other0.2040.21307
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2887
X-RAY DIFFRACTIONr_nbtor_other0.0880.21065
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.261
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2990.249
X-RAY DIFFRACTIONr_mcbond_it1.91331241
X-RAY DIFFRACTIONr_mcbond_other0.4933461
X-RAY DIFFRACTIONr_mcangle_it2.82551842
X-RAY DIFFRACTIONr_scbond_it5.2698840
X-RAY DIFFRACTIONr_scangle_it6.86611729
Refine LS restraints NCS

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

Ens-IDNumberTypeRms dev position (Å)Weight position
1102TIGHT POSITIONAL0.060.05
1162LOOSE POSITIONAL0.375
1102TIGHT THERMAL0.170.5
1162LOOSE THERMAL2.5910
2484TIGHT POSITIONAL0.090.05
2613LOOSE POSITIONAL0.395
2484TIGHT THERMAL0.230.5
2613LOOSE THERMAL2.4110
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 42 -
Rwork0.275 762 -
all-804 -
obs--100 %
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)
12.60050.42720.35384.39160.17452.221-0.1630.10680.2979-0.20190.09430.0093-0.29310.02720.0687-0.07890.09180.0091-0.08150.0157-0.1681-9.48123.131814.4154
22.35332.1711-1.08894.5498-1.61992.0721-0.10940.0627-0.2238-0.62530.0233-0.02970.4786-0.01790.0862-0.00410.08130.0082-0.1232-0.0144-0.2023-2.5965-10.177613.4448
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 1111 - 112
2X-RAY DIFFRACTION2BB0 - 1111 - 112

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