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- PDB-2p4o: CRYSTAL STRUCTURE OF A PUTATIVE LACTONASE OF THE SMP-30/GLUCONOLA... -

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Entry
Database: PDB / ID: 2p4o
TitleCRYSTAL STRUCTURE OF A PUTATIVE LACTONASE OF THE SMP-30/GLUCONOLACTONASE/LRE-LIKE REGION FAMILY (NPUN_F0524) FROM NOSTOC PUNCTIFORME PCC 73102 AT 1.90 A RESOLUTION
Componentshypothetical protein
KeywordsHYDROLASE / PUTATIVE LACTONASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology: / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Mainly Beta / ACETATE ION / Gluconolactonase
Function and homology information
Biological speciesNostoc punctiforme (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (ZP_00111901.1) from Nostoc punctiforme PCC 73102 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 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 1.5Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 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 999 SEQUENCE 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 THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT DATABASE AT THE TIME OF DEPOSITION. 3. THE SEQUENCE IS AVAILABLE FROM GENBANK UNDER ACCESSION ID ZP_00111901.1 AND FROM THE UNIPROT ARCHIVE UNDER ACCESSION ID UPI000038C6E7.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7643
Polymers32,6131
Non-polymers1512
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.442, 91.442, 75.188
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
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: 32612.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme (bacteria) / Strain: PCC 73102 / Gene: ZP_00111901.1 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: B2J846*PLUS
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 48.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: NANODROP, 1.7M (NH4)2SO4, 15.0% Glycerol, 1.7% PEG 400, 0.1M HEPES pH 7.5, 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: 0.91162, 0.97895, 0.97925
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 11, 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
10.911621
20.978951
30.979251
ReflectionResolution: 1.9→29.696 Å / Num. obs: 25746 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-1.957.20.75211343318650.752100
1.95-27.30.5581.41332718280.558100
2-2.067.30.4421.81279317570.442100
2.06-2.127.20.3292.31242717250.329100
2.12-2.197.30.26231222116780.262100
2.19-2.277.20.2313.31176916270.231100
2.27-2.367.30.1794.31123915490.179100
2.36-2.457.30.1574.81105715210.157100
2.45-2.567.20.1395.21051114520.139100
2.56-2.697.20.1195.91012614020.119100
2.69-2.837.20.0987951813180.098100
2.83-37.20.0857.6905912560.085100
3-3.217.10.0797.8847711910.079100
3.21-3.477.10.0748.2791211210.074100
3.47-3.87.10.0659.3726010290.065100
3.8-4.2570.05311.565029350.053100
4.25-4.916.90.04812.558108480.048100
4.91-6.016.80.04712.448807220.047100
6.01-8.56.50.04114.837775830.041100
8.5-29.75.70.03716.219313390.03797

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SOLVEphasing
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→29.696 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.949 / SU B: 7.068 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.133
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. GOL IS MODELED BASED ON CRYSTALLIZATION CONDITIONS. 5. ACT IS MODELED IN THE PUTATIVE ACTIVE SITE. 6. RAMACHANDRAN OUTLIER ASP 214 IS SUPPORTED BY DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1307 5.1 %RANDOM
Rwork0.172 ---
all0.174 ---
obs0.174 25661 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.328 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2246 0 10 134 2390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222336
X-RAY DIFFRACTIONr_bond_other_d0.0010.022146
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.9743209
X-RAY DIFFRACTIONr_angle_other_deg0.86634996
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2735311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.54625.22788
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91315345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.635157
X-RAY DIFFRACTIONr_chiral_restr0.0960.2384
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022629
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02431
X-RAY DIFFRACTIONr_nbd_refined0.2110.2387
X-RAY DIFFRACTIONr_nbd_other0.1850.22196
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21146
X-RAY DIFFRACTIONr_nbtor_other0.0860.21394
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2134
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5980.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.160.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3140.25
X-RAY DIFFRACTIONr_mcbond_it2.1531612
X-RAY DIFFRACTIONr_mcbond_other0.553615
X-RAY DIFFRACTIONr_mcangle_it3.06152484
X-RAY DIFFRACTIONr_scbond_it5.4928883
X-RAY DIFFRACTIONr_scangle_it7.00211720
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 99 -
Rwork0.219 1713 -
obs-1812 100 %
Refinement TLS params.Method: refined / Origin x: 22.388 Å / Origin y: 31.339 Å / Origin z: 19.633 Å
111213212223313233
T0.1542 Å2-0.0183 Å20.0854 Å2--0.2125 Å2-0.0032 Å2---0.1438 Å2
L0.6606 °2-0.1967 °20.1153 °2-2.7309 °20.206 °2--0.7206 °2
S-0.0225 Å °0.0305 Å °0.0261 Å °0.3754 Å °-0.0383 Å °0.1564 Å °-0.0615 Å °-0.0032 Å °0.0608 Å °
Refinement TLS groupSelection: ALL

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