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- PDB-2o62: CRYSTAL STRUCTURE OF A PROTEIN WITH UNKNOWN FUNCTION FROM DUF3598... -

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Basic information

Entry
Database: PDB / ID: 2o62
TitleCRYSTAL STRUCTURE OF A PROTEIN WITH UNKNOWN FUNCTION FROM DUF3598 FAMILY (NPUN_R4044) FROM NOSTOC PUNCTIFORME PCC 73102 AT 1.75 A RESOLUTION
Componentshypothetical protein
KeywordsUNKNOWN FUNCTION / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


regulation of division septum assembly / cell division
Similarity search - Function
Domain of unknown function DUF3598, Biogenesis factor required for ATP synthase 1-like / Domain of unknown function (DUF3598), N-terminal / Cell division topological specificity factor MinE / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DUF3598 domain-containing protein
Similarity search - Component
Biological speciesNostoc punctiforme (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (ZP_00105914.2) from Nostoc punctiforme PCC 73102 at 1.75 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ...BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999SEQUENCE (1) THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE (1) THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE, FOLLOWED BY THE TARGET SEQUENCE. (2) THE SEQUENCE OF THE PROTEIN WAS NOT AVAILABLE AT UNP DATABASE AT THE TIME OF PROCESSING. (3) THE SEQUENCE IS AVAILABLE FROM GENBANK UNDER ACCESSION ID ZP_00105914.2 AND FROM THE UNIPROT ARCHIVE UNDER ACCESSION ID UPI000045C1C7.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,45019
Polymers60,9982
Non-polymers1,45217
Water9,116506
1
A: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,30711
Polymers30,4991
Non-polymers80810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1448
Polymers30,4991
Non-polymers6457
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.210, 71.880, 132.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein hypothetical protein /


Mass: 30499.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme (bacteria) / Strain: PCC 73102 / Gene: ZP_00105914.2 / Production host: Escherichia coli (E. coli) / References: UniProt: B2J6L8*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 506 / 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: 2.39 Å3/Da / Density % sol: 48.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6.3
Details: 0.2M NH4Cl, 20.0% PEG-3350, No Buffer pH 6.3, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97939
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 20, 2006 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 1.75→29.148 Å / Num. obs: 56361 / % possible obs: 93.7 % / Biso Wilson estimate: 24.116 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 9.71
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsDiffraction-ID% possible all
1.75-1.810.4621.614596170.4
1.81-1.890.3832.423510180.4
1.89-1.970.2923.726700189.3
1.97-2.070.2445.239530198.9
2.07-2.20.2026.443832199.8
2.2-2.370.1697.643734199.9
2.37-2.610.1349.244214199.9
2.61-2.990.09712.444060199.9
2.99-29.10.05418.943890199.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
XDSdata reduction
SHARPphasing
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→29.148 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.28 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.114
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. CHLORINE AND GLYCEROL MODELED BASED ON CRYSTALLIZATION CONDITIONS. 5. RESIDUES B182-186 HAVE VERY POOR DENSITY, AND WERE MODELED BASED ON THE CORRESPONDING RESDIUES IN CHAIN A.
RfactorNum. reflection% reflectionSelection details
Rfree0.208 2834 5 %RANDOM
Rwork0.166 ---
obs0.168 56308 93.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.992 Å2
Baniso -1Baniso -2Baniso -3
1-2.08 Å20 Å20 Å2
2---1.18 Å20 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4225 0 92 506 4823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224440
X-RAY DIFFRACTIONr_bond_other_d0.0020.024106
X-RAY DIFFRACTIONr_angle_refined_deg1.6411.9816004
X-RAY DIFFRACTIONr_angle_other_deg0.82839520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7065556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.78323.832214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50715756
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3691541
X-RAY DIFFRACTIONr_chiral_restr0.1020.2668
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024927
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02916
X-RAY DIFFRACTIONr_nbd_refined0.2220.2626
X-RAY DIFFRACTIONr_nbd_other0.2040.24346
X-RAY DIFFRACTIONr_nbtor_refined0.1760.22072
X-RAY DIFFRACTIONr_nbtor_other0.0840.23076
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2345
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2760.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2470.288
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.220
X-RAY DIFFRACTIONr_mcbond_it1.0591.52783
X-RAY DIFFRACTIONr_mcbond_other0.2671.51118
X-RAY DIFFRACTIONr_mcangle_it1.63624338
X-RAY DIFFRACTIONr_scbond_it2.64531873
X-RAY DIFFRACTIONr_scangle_it4.1744.51656
LS refinement shellResolution: 1.748→1.794 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 164 -
Rwork0.246 2888 -
obs-3052 70.34 %
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)
10.65850.458-0.22831.4993-0.20220.56350.032-0.068-0.00580.0363-0.0325-0.167-0.03630.13860.0005-0.06740.00690.004-0.07590.0033-0.094715.54316.63131.559
20.69030.4863-0.03891.47810.0791.35070.001-0.0022-0.05710.0228-0.00840.16050.0233-0.08050.0073-0.07860.01570.0015-0.11490.0026-0.08740.0244.62327.64
30.66580.1889-0.00772.3142-0.3991.43530.01630.0237-0.1117-0.021-0.03450.13760.1425-0.10460.0182-0.1040.0052-0.0077-0.0549-0.0043-0.072316.784-4.03659.427
41.34290.3530.59681.86920.51641.01040.01150.10790.0886-0.1314-0.0157-0.1244-0.10490.22550.0042-0.0847-0.00430.0265-0.02360.0204-0.064531.4269.40762.161
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA2 - 1323 - 133
22AA133 - 269134 - 270
33BB2 - 1323 - 133
44BB133 - 269134 - 270

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