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- PDB-1vl7: Crystal structure of a putative heme oxygenase (alr5027) from nos... -

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Basic information

Entry
Database: PDB / ID: 1vl7
TitleCrystal structure of a putative heme oxygenase (alr5027) from nostoc sp. pcc 7120 at 1.50 A resolution
Componentshypothetical protein alr5027
KeywordsOXIDOREDUCTASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homologyHeme utilization protein HutZ / Pyridoxamine 5'-phosphate oxidase, putative / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta / Alr5027 protein
Function and homology information
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (alr5027) from Nostoc sp. at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999 SEQUENCE THE CONSTRUCT USED FOR EXPRESSION COMPRISED A N-TERMINAL PURIFICATION TAG [MGSDKIHHHHHH] ... SEQUENCE THE CONSTRUCT USED FOR EXPRESSION COMPRISED A N-TERMINAL PURIFICATION TAG [MGSDKIHHHHHH] FOLLOWED BY RESIDUES 1-145 THE PREDICTED GENE PRODUCT OF 17134165. RESIDUES 146-165 WERE OMITTED FROM THE CONSTRUCT TO ELIMINATE A REGION PREDICTED TO BE DISORDERED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein alr5027
B: hypothetical protein alr5027
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,27310
Polymers35,7762
Non-polymers4978
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-2 kcal/mol
Surface area12690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.001, 100.326, 47.667
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-285-

HOH

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Components

#1: Protein hypothetical protein alr5027


Mass: 17888.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Gene: alr5027 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YMA7
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.2 Å3/Da / Density % sol: 43.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop
Details: 0.04M Tris_base, 0.06M Tris Cl, 23% PEG MME 5000 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.000042
DetectorType: ADSC / Detector: CCD / Date: Apr 2, 2004
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000042 Å / Relative weight: 1
ReflectionResolution: 1.5→43.05 Å / Num. obs: 50714 / % possible obs: 99.64 % / Redundancy: 4.68 % / Biso Wilson estimate: 25.18 Å2 / Rsym value: 0.048 / Net I/σ(I): 30.31
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.88 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 4884 / Rsym value: 0.68 / % possible all: 97.62

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0000refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1g76

1g76


Resolution: 1.5→43.05 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.403 / SU ML: 0.045 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18276 2570 5.1 %RANDOM
Rwork0.15443 ---
obs0.15589 48092 99.53 %-
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: 23.707 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2--0.97 Å20 Å2
3----1.09 Å2
Refinement stepCycle: LAST / Resolution: 1.5→43.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2139 0 32 269 2440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222295
X-RAY DIFFRACTIONr_bond_other_d0.0010.022098
X-RAY DIFFRACTIONr_angle_refined_deg1.7491.9253111
X-RAY DIFFRACTIONr_angle_other_deg0.87434845
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6725290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.06624.188117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65415369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9221516
X-RAY DIFFRACTIONr_chiral_restr0.1120.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022604
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02506
X-RAY DIFFRACTIONr_nbd_refined0.220.2390
X-RAY DIFFRACTIONr_nbd_other0.1890.22281
X-RAY DIFFRACTIONr_nbtor_other0.0870.21485
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2180
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1850.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.218
X-RAY DIFFRACTIONr_mcbond_it2.46831488
X-RAY DIFFRACTIONr_mcbond_other0.5793576
X-RAY DIFFRACTIONr_mcangle_it3.0752275
X-RAY DIFFRACTIONr_scbond_it4.7248964
X-RAY DIFFRACTIONr_scangle_it6.55511829
LS refinement shellResolution: 1.498→1.537 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 199 5.65 %
Rwork0.26 3326 -
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)
10.29040.0777-0.10530.2851-0.26311.30030.0350.01710.0472-0.0084-0.0007-0.0036-0.1299-0.1058-0.0344-0.08340.01150.0083-0.08580.0113-0.06756.573323.0852-4.0513
20.99890.31580.0020.8758-0.28411.4492-0.0115-0.0283-0.07820.03010.0029-0.06730.13660.10530.0086-0.1662-0.0034-0.0036-0.1868-0.0028-0.146412.73598.522310.6277
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 11 - 145 / Label seq-ID: 23 - 157

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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