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- PDB-2i02: CRYSTAL STRUCTURE OF a pyridoxamine 5'-phosphate oxidase-like fam... -

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Basic information

Entry
Database: PDB / ID: 2i02
TitleCRYSTAL STRUCTURE OF a pyridoxamine 5'-phosphate oxidase-like family protein (NPUN_R6570) FROM NOSTOC PUNCTIFORME PCC 73102 AT 1.80 A RESOLUTION
Componentsgeneral stress protein of COG3871
KeywordsOXIDOREDUCTASE / GENERAL STRESS PROTEIN OF COG3871 / PYRIDOXAMINE 5'-PHOSPHATE OXIDASE-LIKE FAMILY PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


General stress protein, FMN-binding split barrel domain / Pyridoxamine 5'-phosphate oxidase like / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Pyridoxamine 5'-phosphate oxidase-related, FMN-binding / Alr3246 protein
Similarity search - Component
Biological speciesNostoc punctiforme (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of general stress protein of COG3871 (ZP_00108720.1) from Nostoc punctiforme PCC 73102 at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: 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 1.4Jan 25, 2023Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: general stress protein of COG3871
B: general stress protein of COG3871
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6046
Polymers34,4592
Non-polymers1,1454
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-36 kcal/mol
Surface area13480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.646, 103.646, 109.695
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11B-167-

HOH

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Components

#1: Protein general stress protein of COG3871


Mass: 17229.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme (bacteria) / Strain: PCC 73102 / Gene: ZP_00108720.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YS45, UniProt: B2J0D8*PLUS
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330 / Polyethylene glycol


Mass: 326.383 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.38 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 277 K / pH: 4.5
Details: 0.2M NaCl, 40.0% PEG-300, 0.1M Acetate pH 4.5, 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: 0.979197,0.918370
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 2, 2006 / 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
10.9791971
20.918371
ReflectionResolution: 1.8→29.921 Å / Num. obs: 32823 / % possible obs: 100 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 4.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.8510.60.9460.82529623770.946100
1.85-1.910.60.7311.12451123110.731100
1.9-1.9510.60.5431.42400522620.543100
1.95-2.0110.60.4351.82321321870.435100
2.01-2.0810.60.362.12257021360.36100
2.08-2.1510.60.3032.52186220680.303100
2.15-2.2310.60.25532093419830.255100
2.23-2.3210.50.2053.72033519380.205100
2.32-2.4310.40.1814.21922118420.181100
2.43-2.5510.50.1614.71855217720.161100
2.55-2.6810.40.1345.51759116940.134100
2.68-2.8510.30.1136.51665816100.113100
2.85-3.0410.30.0868.11566815270.086100
3.04-3.2910.20.0798.21436314130.079100
3.29-3.6100.0758.21319513140.075100
3.6-4.029.70.0678.91163812000.067100
4.02-4.6590.078.3967510740.07100
4.65-5.699.70.0658.989809250.065100
5.69-8.059.90.05711.273137410.057100
8.05-29.928.50.04512.338294490.04598.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→29.921 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.503 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.107
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. RESIDUES A1-4, A46-48, B1-4, AND B136-138 ARE DISORDERED AND NOT INCLUDED IN THE MODEL. 4. RESIDUES B45-48 AND B61 ARE POORLY ORDERED. 5. MOLECULES FMN AND PEG-300 (P33) ARE MODELED. 6. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 7. UNEXPLAINED DENSITY OBSERVED NEAR RESIDUES A58, A98, A101, B31-32, B61, B67.
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1663 5.1 %RANDOM
Rwork0.177 ---
all0.178 ---
obs-32793 99.99 %-
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: 25.749 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å2-0.27 Å20 Å2
2---0.55 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2262 0 53 175 2490
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222445
X-RAY DIFFRACTIONr_bond_other_d0.0010.021633
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.9543329
X-RAY DIFFRACTIONr_angle_other_deg0.8834014
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2425294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.58425.128117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20915418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.334157
X-RAY DIFFRACTIONr_chiral_restr0.0850.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022657
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02473
X-RAY DIFFRACTIONr_nbd_refined0.220.2454
X-RAY DIFFRACTIONr_nbd_other0.1990.21661
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21157
X-RAY DIFFRACTIONr_nbtor_other0.0880.21272
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2148
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.221
X-RAY DIFFRACTIONr_mcbond_it2.3631490
X-RAY DIFFRACTIONr_mcbond_other0.5683567
X-RAY DIFFRACTIONr_mcangle_it3.39352344
X-RAY DIFFRACTIONr_scbond_it5.21581164
X-RAY DIFFRACTIONr_scangle_it7.24511976
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 107 -
Rwork0.21 2258 -
obs-2365 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.24440.20080.51951.54270.60231.61240.0180.2510.13-0.21640.0291-0.1648-0.11790.176-0.0471-0.0412-0.01790.0245-0.01260.0174-0.031628.99725.11915.445
21.51090.2729-0.01510.31170.06511.07020.01140.1590.1698-0.1101-0.00340.0602-0.1216-0.0855-0.008-0.03580.0154-0.0007-0.03210.0134-0.03185.98725.86716.087
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA5 - 456 - 46
21AA49 - 14750 - 148
32BB5 - 1356 - 136
42BB139 - 147140 - 148

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