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- PDB-2qdr: Crystal structure of a putative dioxygenase (npun_f5605) from nos... -

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Basic information

Entry
Database: PDB / ID: 2qdr
TitleCrystal structure of a putative dioxygenase (npun_f5605) from nostoc punctiforme pcc 73102 at 2.60 A resolution
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Double-stranded beta-helix fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Protein of unknown function DUF4437 / Domain of unknown function (DUF4437) / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Unknown ligand / DUF4437 domain-containing protein
Similarity search - Component
Biological speciesNostoc punctiforme (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of uncharacterized protein (ZP_00345151.1) from Nostoc punctiforme PCC 73102 at 2.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 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: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jul 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
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUGGESTS AN OCTAMER AS A SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE 1. THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT DATABASE AT THE TIME OF ... SEQUENCE 1. THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT DATABASE AT THE TIME OF DEPOSITION. THE SEQUENCE INFORMATION IS AVAILABLE AT GENBANK WITH ACCESSION CODE ZP_00345151.1 AND FROM THE UNIPROT ARCHIVE UNDER ACCESSION ID UPI000045C072. 2. 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,4918
Polymers69,5382
Non-polymers9536
Water59433
1
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,96632
Polymers278,1538
Non-polymers3,81324
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation11_655-x+y+1,y,-z1
Unit cell
Length a, b, c (Å)102.096, 102.096, 250.807
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 2

Dom-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1PHEGLNAA16 - 30017 - 301
2HISASPBB18 - 30119 - 302
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUGGESTS AN OCTAMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Uncharacterized protein


Mass: 34769.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme (bacteria) / Strain: PCC 73102 / Gene: ZP_00345151.1 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: B2J7U5*PLUS
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.71 Å3/Da / Density % sol: 54.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.33
Details: NANODROP, 21.4% Ethanol, 0.2M Magnesium chloride, 0.1M HEPES pH 7.33, 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, 0.97916, 0.97883
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 7, 2007 / 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
10.918371
20.979161
30.978831
ReflectionResolution: 2.6→47.298 Å / Num. obs: 24629 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 70.689 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 10.68
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.6-2.690.0121.6328974326198.8
2.69-2.80.0122.23544345631100
2.8-2.930.0122.83596146221100
2.93-3.080.0123.73389943611100
3.08-3.270.0125.63475644591100
3.27-3.520.0127.93508845021100
3.52-3.880.01210.5346984470197.7
3.88-4.430.01218.43497844801100
4.43-5.570.01223.33536045151100
5.57-47.2980.01230.1357614602199.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→47.298 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.909 / SU B: 27.995 / SU ML: 0.273 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.613 / ESU R Free: 0.336
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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. ELECTRON DENSITIES FOR RESIDUES 1-15 AND 301-302 IN THE A SUBUNIT, AND RESIDUES 1-17 AND 302 IN THE B-SUBUNIT WERE DISORDERED. THEREFORE, THESE RESIDUES WERE NOT MODELED. 5. 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID (HEPES) MOLECULES FROM THE CRYSTALLIZATION SOLUTIONS WERE MODELED INTO THE STRUCTURE. 6. UNKNOWN LIGANDS (UNL) WERE MODELED IN THE PUTATIVE ACTIVE SITES NEAR THE SIDECHAIN OF HIS 272 ON BOTH SUBUNITS OF THE ASYMMETRIC UNIT.
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1252 5.1 %RANDOM
Rwork0.24 ---
obs0.242 24591 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 60.231 Å2
Baniso -1Baniso -2Baniso -3
1-2.89 Å21.44 Å20 Å2
2--2.89 Å20 Å2
3----4.33 Å2
Refinement stepCycle: LAST / Resolution: 2.6→47.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4500 0 58 33 4591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224684
X-RAY DIFFRACTIONr_bond_other_d0.0030.024132
X-RAY DIFFRACTIONr_angle_refined_deg1.8241.9486374
X-RAY DIFFRACTIONr_angle_other_deg1.23539569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.0785571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.06223.439221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.80315717
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.891531
X-RAY DIFFRACTIONr_chiral_restr0.070.2654
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025252
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021011
X-RAY DIFFRACTIONr_nbd_refined0.1530.3802
X-RAY DIFFRACTIONr_nbd_other0.1280.34009
X-RAY DIFFRACTIONr_nbtor_refined0.1720.52210
X-RAY DIFFRACTIONr_nbtor_other0.080.52579
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.230.5213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1110.317
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1320.378
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.54
X-RAY DIFFRACTIONr_mcbond_it132988
X-RAY DIFFRACTIONr_mcbond_other0.26431164
X-RAY DIFFRACTIONr_mcangle_it1.44354534
X-RAY DIFFRACTIONr_scbond_it2.64182113
X-RAY DIFFRACTIONr_scangle_it3.683111838
Refine LS restraints NCS

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

NumberTypeRms dev position (Å)Weight position
1651TIGHT POSITIONAL0.030.05
2561MEDIUM POSITIONAL0.280.5
1651TIGHT THERMAL0.060.5
2561MEDIUM THERMAL0.392
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.454 94 -
Rwork0.407 1663 -
obs-1757 98.76 %
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)
11.01760.07011.53621.5426-0.19363.2921-0.0867-0.13460.32430.19670.01640.0447-0.3516-0.28360.07020.00220.09720.0864-0.0851-0.02790.197125.09224.78316.844
21.96080.18211.73992.20980.03081.55170.003-0.07320.05290.16480.0442-0.135-0.00830.0354-0.0472-0.0260.0540.0224-0.1853-0.02690.062439.36913.11522.977
32.4287-0.64521.24371.3691-0.31392.37170.003-0.1664-0.2246-0.05660.14230.15160.2989-0.1106-0.1453-0.0175-0.044-0.0091-0.15840.08720.122633.893-24.75426.574
41.14630.58490.43011.6533-0.14431.54760.04240.07760.0251-0.12930.09840.1011-0.0063-0.0205-0.1408-0.0247-0.0393-0.0455-0.19360.0660.106328.095-12.79511.802
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA16 - 20517 - 206
2X-RAY DIFFRACTION2AA206 - 300207 - 301
3X-RAY DIFFRACTION3BB18 - 20319 - 204
4X-RAY DIFFRACTION4BB204 - 301205 - 302

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