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- PDB-4r01: Crystal structure of SP1627, a putative NADH-flavin reductase, fr... -

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Basic information

Entry
Database: PDB / ID: 4r01
TitleCrystal structure of SP1627, a putative NADH-flavin reductase, from Streptococcus pneumoniae TIGR4
Componentsputative NADH-flavin reductase
KeywordsOXIDOREDUCTASE / structural genomics / CSGID / Center for Structural Genomics of Infectious Diseases / NIAID / National Institute for Allergy and Infectious Diseases / alpha/beta fold / NAD(P) dinucleotide-binding Rossmann fold / putative NADH-flavin reductase / putative oxidoreductase
Function / homologyNAD(P)H-binding / NAD(P)-binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / NAD(P)-bd_dom domain-containing protein / NAD(P)-bd_dom domain-containing protein
Function and homology information
Biological speciesStreptococcus pneumoniae TIGR4 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsStogios, P.J. / Onopriyenko, O. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of SP1627, a putative NADH-flavin reductase, from Streptococcus pneumoniae TIGR4
Authors: Stogios, P.J. / Onopriyenko, O. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJul 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative NADH-flavin reductase
B: putative NADH-flavin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4809
Polymers46,0502
Non-polymers4307
Water2,954164
1
A: putative NADH-flavin reductase
B: putative NADH-flavin reductase
hetero molecules

A: putative NADH-flavin reductase
B: putative NADH-flavin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,96018
Polymers92,1004
Non-polymers86014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area7850 Å2
ΔGint-180 kcal/mol
Surface area34970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.030, 82.960, 43.790
Angle α, β, γ (deg.)90.00, 105.56, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-424-

HOH

21B-470-

HOH

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Components

#1: Protein putative NADH-flavin reductase


Mass: 23025.029 Da / Num. of mol.: 2 / Fragment: SP1627
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae TIGR4 (bacteria)
Strain: TIGR4 / Gene: SP_1627 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97PI8, UniProt: A0A0H2UR89*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 3.04 Å3/Da / Density % sol: 59.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2 M Ammonium Sulfate, 0.1 M Bis-Tris Propane, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 10, 2014
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 29142 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 25.55
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.15 / % possible all: 96.7

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Processing

Software
NameVersionClassification
HKL-3000data collection
BALBESphasing
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H2S

3h2s


Resolution: 2.4→29.577 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2418 1384 6.83 %random
Rwork0.1855 ---
obs0.1893 20249 93.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→29.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3246 0 19 164 3429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053319
X-RAY DIFFRACTIONf_angle_d0.7874492
X-RAY DIFFRACTIONf_dihedral_angle_d14.7371222
X-RAY DIFFRACTIONf_chiral_restr0.032521
X-RAY DIFFRACTIONf_plane_restr0.004577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.48580.34361340.26351804X-RAY DIFFRACTION90
2.4858-2.58520.30781350.26781827X-RAY DIFFRACTION89
2.5852-2.70280.32831320.25471821X-RAY DIFFRACTION93
2.7028-2.84520.33351380.2421865X-RAY DIFFRACTION93
2.8452-3.02330.33221390.23971897X-RAY DIFFRACTION94
3.0233-3.25650.26851410.22841887X-RAY DIFFRACTION95
3.2565-3.58370.25961450.1871936X-RAY DIFFRACTION95
3.5837-4.10110.21451410.15671950X-RAY DIFFRACTION96
4.1011-5.16240.16681430.1371939X-RAY DIFFRACTION96
5.1624-29.57920.20031360.15141939X-RAY DIFFRACTION93
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)
14.7486-1.45780.83025.785-1.4075.72310.2293-0.003-1.0076-0.3233-0.8496-0.50930.23230.70820.56620.32130.07480.06710.39610.11530.579724.5621-3.129215.238
25.8989-0.305-2.62391.3432-1.03826.67420.084-0.1956-0.8059-0.1169-0.17240.02680.16290.50390.15960.40010.12440.03190.35580.08520.631628.6845-2.123415.3993
39.2932-2.66340.43393.944-4.7456.6455-0.55280.37-0.10870.94430.3278-0.3101-0.31330.6480.01180.38380.10460.00920.44-0.01960.42624.25673.681310.0061
44.809-0.8491-0.47741.95330.09912.57830.12220.4443-0.4154-0.2255-0.2656-0.08490.15810.05070.14370.3030.04590.00320.2453-0.02130.325310.00853.822711.1461
58.3536-3.5355-3.11039.73770.43976.1994-0.42950.48970.4544-0.22150.4627-0.2547-0.52140.1907-0.10890.3436-0.127-0.02390.31790.05340.507818.728935.760328.1046
66.82781.2907-0.6086.8429-0.44213.19760.0114-0.05240.5936-0.15360.1596-0.338-0.16910.1637-0.17910.3281-0.1261-0.04270.3565-0.00320.405624.081234.029729.1651
77.10844.90154.93058.08256.13624.60530.0118-0.524-0.18760.4556-0.0108-0.15550.10070.2109-0.07790.3076-0.0306-0.03040.37620.08680.343820.032620.103633.1436
85.45091.59520.47443.83380.14152.23160.0101-0.380.49630.1342-0.05420.1708-0.1047-0.17290.04550.2613-0.010.01280.3429-0.02810.21244.287327.998533.2546
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 0:11 )A0 - 11
2X-RAY DIFFRACTION2( CHAIN A AND RESID 12:54 )A12 - 54
3X-RAY DIFFRACTION3( CHAIN A AND RESID 55:71 )A55 - 71
4X-RAY DIFFRACTION4( CHAIN A AND RESID 72:209 )A72 - 209
5X-RAY DIFFRACTION5( CHAIN B AND RESID 0:16 )B0 - 16
6X-RAY DIFFRACTION6( CHAIN B AND RESID 17:67 )B17 - 67
7X-RAY DIFFRACTION7( CHAIN B AND RESID 68:91 )B68 - 91
8X-RAY DIFFRACTION8( CHAIN B AND RESID 92:209 )B92 - 209

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