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- PDB-3dee: CRYSTAL STRUCTURE OF A PUTATIVE REGULATORY PROTEIN INVOLVED IN TR... -

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Basic information

Entry
Database: PDB / ID: 3dee
TitleCRYSTAL STRUCTURE OF A PUTATIVE REGULATORY PROTEIN INVOLVED IN TRANSCRIPTION (NGO1945) FROM NEISSERIA GONORRHOEAE FA 1090 AT 2.25 A RESOLUTION
ComponentsPutative regulatory protein
KeywordsTRANSCRIPTION / PUTATIVE REGULATORY PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


DUF2063 / Outer Surface Protein A; domain 3 - #50 / Putative DNA-binding domain, bacteria / DUF2063, N-terminal superfamily / : / Putative DNA-binding domain / NGO1945 C-terminal domain / Outer Surface Protein A; domain 3 / DNA polymerase; domain 1 / Alpha-Beta Complex ...DUF2063 / Outer Surface Protein A; domain 3 - #50 / Putative DNA-binding domain, bacteria / DUF2063, N-terminal superfamily / : / Putative DNA-binding domain / NGO1945 C-terminal domain / Outer Surface Protein A; domain 3 / DNA polymerase; domain 1 / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / Uncharacterized protein
Similarity search - Component
Biological speciesNeisseria gonorrhoeae FA 1090 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation.
Authors: Das, D. / Grishin, N.V. / Kumar, A. / Carlton, D. / Bakolitsa, C. / Miller, M.D. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Burra, P. / Chen, C. / Chiu, H.J. / Chiu, M. / Clayton, T. / ...Authors: Das, D. / Grishin, N.V. / Kumar, A. / Carlton, D. / Bakolitsa, C. / Miller, M.D. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Burra, P. / Chen, C. / Chiu, H.J. / Chiu, M. / Clayton, T. / Deller, M.C. / Duan, L. / Ellrott, K. / Ernst, D. / Farr, C.L. / Feuerhelm, J. / Grzechnik, A. / Grzechnik, S.K. / Grant, J.C. / Han, G.W. / Jaroszewski, L. / Jin, K.K. / Johnson, H.A. / Klock, H.E. / Knuth, M.W. / Kozbial, P. / Krishna, S.S. / Marciano, D. / McMullan, D. / Morse, A.T. / Nigoghossian, E. / Nopakun, A. / Okach, L. / Oommachen, S. / Paulsen, J. / Puckett, C. / Reyes, R. / Rife, C.L. / Sefcovic, N. / Tien, H.J. / Trame, C.B. / van den Bedem, H. / Weekes, D. / Wooten, T. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionJun 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
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
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1454
Polymers29,0051
Non-polymers1403
Water1,71195
1
A: Putative regulatory protein
hetero molecules

A: Putative regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2918
Polymers58,0112
Non-polymers2806
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2810 Å2
ΔGint-62 kcal/mol
Surface area21630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.522, 31.879, 86.369
Angle α, β, γ (deg.)90.000, 115.800, 90.000
Int Tables number5
Space group name H-MC121
DetailsAUTHORS STATE THAT THE PROTOMER MAY FORM A DIMER BASED ON CRYSTAL PACKING ANALYSIS.

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Components

#1: Protein Putative regulatory protein


Mass: 29005.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae FA 1090 (bacteria)
Gene: YP_208969.1, NGO1945 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5F5I0
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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. DNA SEQUENCING OF THE CLONED CONSTRUCT SHOWS A LEUCINE AT POSITION 94 INSTEAD OF A PROLINE. THE LEUCINE AT POSITION 94 IS SUPPORTED BY THE ELECTRON DENSITY.

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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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.36
Details: 0.2M magnesium chloride, 8.2% Ethanol, 0.1M Imidazole pH 8.36, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97929
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 1, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979291
ReflectionResolution: 2.1→77.85 Å / Num. obs: 13583 / % possible obs: 87.2 % / Redundancy: 3.1 % / Biso Wilson estimate: 31.24 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.213.10.4751.5680022010.47597.9
2.21-2.353.10.4560.6502416450.45677.7
2.35-2.513.10.2762.5608419640.27698.3
2.51-2.713.10.2162.8448714650.21678.4
2.71-2.973.10.1365521817090.13698.4
2.97-3.323.10.0887.5470515360.08898.8
3.32-3.8330.0669.621707150.06651.2
3.83-4.730.03915.727289000.03976
4.7-6.6430.04115.827569240.04198.8
6.64-77.852.80.04212.714675240.04297.4

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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: 2.1→77.85 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.929 / SU B: 12.389 / SU ML: 0.168 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.269 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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. CHLORIDE AND IMIDAZOLE WERE MODELED BASED ON CRYSTALLIZATION CONDITIONS. 5. THERE IS UNMODELED ELECTRON DENSITY NEAR RESIDUE A169, WHICH COULD BE PART OF THE MISSING N-TERMINUS. 6. REFLECTIONS IN THE FOLLOWING RESOLUTION RANGES CORRESPONDING TO ICE RINGS WERE OMITTED DURING INTEGRATION OF THE DIFFRACTION DATA: 3.97-3.82 A, 3.72-3.61 A, 3.50-3.39 A, 2.69-2.64 A AND 2.26-2.24 A. IN ADDITION, 14 UNUSUALLY STRONG REFLECTIONS WERE ALSO OMITTED FROM THE DATA USED FOR FINAL REFINEMENT. 7. THE NOMINAL RESOLUTION IS 2.25 A WITH 2563 OBSERVED REFLECTIONS BETWEEN 2.25-2.10 (88.8% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.267 660 4.9 %RANDOM
Rwork0.223 ---
obs0.225 13555 86.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.623 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å20 Å2-0.52 Å2
2--3.7 Å20 Å2
3----2.72 Å2
Refinement stepCycle: LAST / Resolution: 2.1→77.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1623 0 7 95 1725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221683
X-RAY DIFFRACTIONr_bond_other_d0.0010.021116
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.9542294
X-RAY DIFFRACTIONr_angle_other_deg0.95632718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1395205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.70624.57883
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.49915277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.332158
X-RAY DIFFRACTIONr_chiral_restr0.0950.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021878
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02355
X-RAY DIFFRACTIONr_nbd_refined0.2020.2381
X-RAY DIFFRACTIONr_nbd_other0.1850.21120
X-RAY DIFFRACTIONr_nbtor_refined0.1850.2840
X-RAY DIFFRACTIONr_nbtor_other0.0870.2784
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.276
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3420.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2130.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.25
X-RAY DIFFRACTIONr_mcbond_it1.13921137
X-RAY DIFFRACTIONr_mcbond_other0.2382400
X-RAY DIFFRACTIONr_mcangle_it1.6331637
X-RAY DIFFRACTIONr_scbond_it0.922763
X-RAY DIFFRACTIONr_scangle_it1.3253654
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 44 -
Rwork0.286 1059 -
all-1103 -
obs--96.33 %
Refinement TLS params.Method: refined / Origin x: -9.3437 Å / Origin y: 7.9975 Å / Origin z: 20.742 Å
111213212223313233
T-0.059 Å20.0324 Å2-0.0092 Å2--0.1308 Å20.0007 Å2---0.0578 Å2
L3.4483 °21.1081 °2-1.7031 °2-0.4741 °2-0.6458 °2--2.1115 °2
S0.1603 Å °0.1961 Å °0.0827 Å °0.0924 Å °0.0184 Å °0.0412 Å °-0.0377 Å °0.1443 Å °-0.1787 Å °

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