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- PDB-3nqn: Crystal structure of a Protein with unknown function. (DR_2006) f... -

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Basic information

Entry
Database: PDB / ID: 3nqn
TitleCrystal structure of a Protein with unknown function. (DR_2006) from DEINOCOCCUS RADIODURANS at 1.88 A resolution
Componentsuncharacterized protein
KeywordsStructural Genomics / Unknown Function / Protein with unknown function / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyUncharacterised protein PF12723, DUF3809 / Protein of unknown function DUF3809 / Protein of unknown function (DUF3809) / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / 2-Layer Sandwich / metal ion binding / Alpha Beta / DUF3809 domain-containing protein
Function and homology information
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.88 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Protein with unknown function. (DR_2006) from DEINOCOCCUS RADIODURANS at 1.88 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 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 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,8388
Polymers33,3632
Non-polymers4756
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-45 kcal/mol
Surface area14520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.509, 53.509, 223.753
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A3 - 156
2116B3 - 156
DetailsCRYSTAL PACKING ANALYSIS AND ANAYLTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORT THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION.

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Components

#1: Protein uncharacterized protein


Mass: 16681.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: DR_2006 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9RSW5
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
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: 2.4 Å3/Da / Density % sol: 48.76 %
Description: THE R MERGE, AND COMPLETENETSS STATISTICS REPORTED IN REMARK 200 WERE COMPUTED WITH XSCALE WITH FRIEDEL PAIRS KEPT SEPARATE.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.0500M calcium chloride, 15.8000% polyethylene glycol 3350, NANODROP, 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: 0.91837,0.97925,0.97883
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 3, 2009 / 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
20.979251
30.978831
ReflectionResolution: 1.88→28.893 Å / Num. obs: 27005 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 27.317 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 13.56
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.88-1.954.50.7541.310892435282.8
1.95-2.030.5252.115583491895.6
2.03-2.120.3942.916132476997.5
2.12-2.230.2824.217003493098.3
2.23-2.370.2235.417309493598.5
2.37-2.550.1567.717426494098.8
2.55-2.810.11110.918021505298.6
2.81-3.210.05919.317499485898.3
3.21-4.040.03233.617912493997.2
4.04-28.8930.02245.818249503897.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0110refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.88→28.893 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 7.371 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.147
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 THE ...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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM THE ASSIGNMENT OF TLS GROUPS. 5. CALCIUM (CA) FROM THE CRYSTALLIZATION AND (4R)-2-METHYL-2,4-PENTANEDIOL (MRD), USED AS A CRYO- PROTECTANT WERE MODELED INTO THE STRUCTURE. 6. ELECTRON DENSITIES CORRESPONDING TO RESIDUES 116-119 ON THE A SUBUNIT AND RESIDUES 117-123 ON THE B SUBUNIT WERE DISORDERED AND THESE REGIONS COULD NOT BE RELIABLY MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1350 5 %RANDOM
Rwork0.196 ---
obs0.199 26914 97.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 84.3 Å2 / Biso mean: 38.951 Å2 / Biso min: 17.85 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å20 Å2
2--1.09 Å20 Å2
3----2.18 Å2
Refinement stepCycle: LAST / Resolution: 1.88→28.893 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 27 190 2434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222501
X-RAY DIFFRACTIONr_bond_other_d0.0010.021729
X-RAY DIFFRACTIONr_angle_refined_deg1.071.9783441
X-RAY DIFFRACTIONr_angle_other_deg0.71634213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8185357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.80522.832113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.48615393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8961527
X-RAY DIFFRACTIONr_chiral_restr0.0810.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212900
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02534
X-RAY DIFFRACTIONr_mcbond_it1.66231592
X-RAY DIFFRACTIONr_mcbond_other0.4613648
X-RAY DIFFRACTIONr_mcangle_it2.71752540
X-RAY DIFFRACTIONr_scbond_it4.5638909
X-RAY DIFFRACTIONr_scangle_it6.711872
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1688 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.475
LOOSE THERMAL2.3810
LS refinement shellResolution: 1.884→1.933 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 88 -
Rwork0.282 1669 -
all-1757 -
obs--88.56 %
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)
10.58280.1006-0.05870.89480.3041.60330.0235-0.0552-0.01680.0907-0.0340.0079-0.00910.01830.01050.0352-0.00460.01420.12230.02820.0894.545114.668243.6087
20.9876-0.1451-0.18070.9528-0.37571.9166-0.01940.0576-0.05130.06670.0238-0.0503-0.0503-0.0025-0.00430.08420.01170.00560.023-0.01560.07083.512214.818280.0261
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 157
2X-RAY DIFFRACTION2B0 - 156

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