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- PDB-2fur: CRYSTAL STRUCTURE OF A PUTATIVE FMN-BINDING PROTEIN (TA1372) FROM... -

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Basic information

Entry
Database: PDB / ID: 2fur
TitleCRYSTAL STRUCTURE OF A PUTATIVE FMN-BINDING PROTEIN (TA1372) FROM THERMOPLASMA ACIDOPHILUM AT 1.80 A RESOLUTION
Componentshypothetical protein
KeywordsFMN-BINDING PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyPyridoxamine 5'-phosphate oxidase-related / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta / : / Uncharacterized protein
Function and homology information
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein 10640715 from Thermoplasma acidophilum at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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
Remark 999SEQUENCE THE ELECTRON DENSITY CLEARLY INDICATES THAT THE RESIDUE AT POSITION 135 IS A TRYPTOPHAN ...SEQUENCE THE ELECTRON DENSITY CLEARLY INDICATES THAT THE RESIDUE AT POSITION 135 IS A TRYPTOPHAN AND NOT AN ARGININE. DNA SEQUENCING OF THE CLONED CONSTRUCT CONFIRMS THIS OBSERVATION. THE STRAIN OF THE SOURCE DNA CLONED IS NOT CERTAIN AND MAY DIFFER FROM THE DSM-1728 STRAIN SEQUENCED IN THE DATABASE.
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY DATA SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,7757
Polymers47,4652
Non-polymers3105
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-38 kcal/mol
Surface area16660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.040, 66.690, 99.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: TYR / End label comp-ID: ILE / Refine code: 6 / Auth seq-ID: 19 - 208 / Label seq-ID: 20 - 209

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein hypothetical protein


Mass: 23732.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: 10640715 / Production host: Escherichia coli (E. coli) / References: GenBank: 10640715, UniProt: Q9HIG7*PLUS
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 43.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5
Details: 10.0% PEG-6000, 0.1M Acetate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9797, 1.0000, 0.9796
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2005
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
211
30.97961
ReflectionResolution: 1.8→29.26 Å / Num. obs: 38245 / % possible obs: 92 % / Redundancy: 1.91 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 7.38
Reflection shell

Rmerge(I) obs: 0.715 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured obsNum. unique obsRsym value% possible all
1.8-1.861.891.6949550120.71572.9
1.86-1.941.9312617660584.4
1.94-2.032.5212392647386.7
2.03-2.133.4712060631492.1
2.13-2.274.613913727094.7
2.27-2.445.7213136683395.7
2.44-2.697.0213794721096.9
2.69-3.079.8913476704198.1
3.07-3.8713.6513968734499.2
3.8719.9913906728198.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
XSCALEdata scaling
PDB_EXTRACT1.7data extraction
XDSdata reduction
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→29.26 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.409 / SU ML: 0.113 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.128
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 ...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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (3) TLS GROUPS WERE ASSIGNED WITH THE AID OF TLSMD.
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1910 5 %RANDOM
Rwork0.186 ---
obs0.188 38187 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.249 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2---1.93 Å20 Å2
3---2.17 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2971 0 20 272 3263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223094
X-RAY DIFFRACTIONr_bond_other_d0.0010.022108
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9754187
X-RAY DIFFRACTIONr_angle_other_deg0.98335177
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0565381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89324.215121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43415548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1151513
X-RAY DIFFRACTIONr_chiral_restr0.0930.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023346
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02599
X-RAY DIFFRACTIONr_nbd_refined0.2070.2523
X-RAY DIFFRACTIONr_nbd_other0.1950.22052
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21448
X-RAY DIFFRACTIONr_nbtor_other0.0870.21631
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2182
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3350.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2280.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1030.215
X-RAY DIFFRACTIONr_mcbond_it2.38332099
X-RAY DIFFRACTIONr_mcbond_other0.6173774
X-RAY DIFFRACTIONr_mcangle_it3.10953128
X-RAY DIFFRACTIONr_scbond_it5.37681296
X-RAY DIFFRACTIONr_scangle_it6.991111059
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2450 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.55
LOOSE THERMAL2.3410
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 138 -
Rwork0.288 2520 -
all-2658 -
obs--95.06 %
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)
12.2442-0.0035-0.43011.1440.71152.11260.0050.1120.109-0.0639-0.07970.2603-0.018-0.04830.0747-0.06120.00210.0103-0.0601-0.0207-0.037511.538232.50393.4916
20.68120.5052-0.14731.07430.38950.3874-0.03580.077-0.1703-0.0889-0.03680.0958-0.0186-0.02660.0726-0.04450.0027-0.0111-0.0438-0.006-0.032915.616429.04543.0669
32.0133-2.7124-0.39765.83510.86560.2449-0.00120.01670.1076-0.08610.0586-0.2087-0.05490.0382-0.0574-0.0456-0.00970.0483-0.04280.001-0.047227.809847.17926.0757
41.64061.06120.38272.49281.72762.3793-0.07690.0616-0.04540.1679-0.14610.4939-0.0411-0.05030.2231-0.02510.01860.0598-0.0317-0.0312-0.0518.485439.995517.8762
51.598-0.6922-0.66961.96680.36650.5369-0.00470.0469-0.10320.1261-0.07330.3374-0.0141-0.04770.078-0.0230.00930.0405-0.0277-0.0177-0.08158.321244.553618.2951
61.732-2.0889-0.63623.26970.90740.7118-0.1235-0.0722-0.0250.23560.1074-0.08470.06050.13490.0161-0.0369-0.00450.0031-0.007-0.012-0.071229.997743.922213.5951
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA16 - 5517 - 56
22AA56 - 16857 - 169
33AA169 - 208170 - 209
44BB19 - 5520 - 56
55BB56 - 16857 - 169
66BB169 - 208170 - 209

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