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- PDB-4heh: Crystal structure of AppA SCHIC domain from Rb. sphaeroides -

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Basic information

Entry
Database: PDB / ID: 4heh
TitleCrystal structure of AppA SCHIC domain from Rb. sphaeroides
ComponentsAppA protein
KeywordsMETAL BINDING PROTEIN / redox sensing / heme binding
Function / homology
Function and homology information


blue light photoreceptor activity / FAD binding
Similarity search - Function
Methionine synthase domain / Sensors of blue-light using FAD / BLUF domain profile. / BLUF domain / Sensors of blue-light using FAD / Cobalamin-binding domain / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Methionine synthase domain / Acylphosphatase-like domain superfamily / Rossmann fold ...Methionine synthase domain / Sensors of blue-light using FAD / BLUF domain profile. / BLUF domain / Sensors of blue-light using FAD / Cobalamin-binding domain / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Methionine synthase domain / Acylphosphatase-like domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsDragnea, V. / Yin, L. / Dann III, C.E. / Bauer, C.E.
CitationJournal: MBio / Year: 2013
Title: Redox and light control the heme-sensing activity of AppA.
Authors: Yin, L. / Dragnea, V. / Feldman, G. / Hammad, L.A. / Karty, J.A. / Dann III, C.E. / Bauer, C.E.
History
DepositionOct 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AppA protein
B: AppA protein


Theoretical massNumber of molelcules
Total (without water)45,5272
Polymers45,5272
Non-polymers00
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-13 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.044, 64.489, 56.772
Angle α, β, γ (deg.)90.000, 96.230, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein AppA protein


Mass: 22763.350 Da / Num. of mol.: 2 / Fragment: SCHIC domain, UNP residues 186-398
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: HR / Gene: appA / Plasmid: pTYB12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q53119
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.16 Å3/Da / Density % sol: 43.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25% PEG 3350, 0.1 M Bis-Tris, 0.1 M NaCl, 10% glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: May 2, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 24575 / Num. obs: 24533 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 36.41 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 34

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→42.47 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.807 / SU ML: 0.3 / σ(F): 0 / Phase error: 26.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1916 8.08 %random
Rwork0.1825 ---
all0.1869 24621 --
obs0.1869 23719 95.97 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.321 Å2 / ksol: 0.326 e/Å3
Displacement parametersBiso max: 142 Å2 / Biso mean: 54.7601 Å2 / Biso min: 21.62 Å2
Baniso -1Baniso -2Baniso -3
1--4.4595 Å2-0 Å2-7.0873 Å2
2--0.8084 Å20 Å2
3---3.6511 Å2
Refinement stepCycle: LAST / Resolution: 2.05→42.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3158 0 0 183 3341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073221
X-RAY DIFFRACTIONf_angle_d0.9444381
X-RAY DIFFRACTIONf_chiral_restr0.054538
X-RAY DIFFRACTIONf_plane_restr0.005566
X-RAY DIFFRACTIONf_dihedral_angle_d12.5481197
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0432-2.09430.35551170.26341353147083
2.0943-2.15090.28171250.21291473159892
2.1509-2.21420.25971320.18731509164194
2.2142-2.28570.26021380.2041522166095
2.2857-2.36730.32211300.21551536166695
2.3673-2.46210.30421410.23051556169795
2.4621-2.57420.27351340.21531563169797
2.5742-2.70980.27641390.21711568170797
2.7098-2.87960.27311390.2021578171798
2.8796-3.10190.29551400.20571598173898
3.1019-3.41390.2371450.19791612175799
3.4139-3.90760.20631420.167116281770100
3.9076-4.9220.19691490.145516381787100
4.922-42.47920.19741450.162816691814100
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)
11.2356-2.69490.48056.0018-1.9257.1370.385-0.3167-0.1423-0.012-0.09931.2328-0.2068-1.0998-0.18380.226-0.03120.05380.3464-0.00920.6619-30.7382-16.9146-2.8567
28.9223-3.11821.68073.70191.42534.5383-0.05540.6983-0.931-0.6654-0.12611.8081-0.2385-0.10220.18930.23170.0303-0.11110.353-0.00660.4606-28.1187-14.5745-12.1347
36.9032-4.79894.57596.1961-5.40134.7225-0.0173-0.7546-0.24130.68980.28450.4543-0.1159-0.8732-0.33140.3835-0.07120.04750.3107-0.02540.2954-23.1912-12.63570.9886
48.43791.8293-3.44617.4653-3.94645.16440.08230.0461-0.5611-0.0015-0.7842-0.43620.41670.30830.67280.3105-0.0211-0.04860.2282-0.07950.2434-18.5491-18.7269-6.1574
56.73982.2776-0.1576.68561.90153.96190.03250.91781.3642-0.6097-0.0473-0.1143-1.4423-0.01820.37250.99740.2277-0.20450.43680.18380.6723-15.73115.8076-15.8294
64.83521.84831.63512.21540.02943.3509-0.17310.69720.3579-0.3983-0.0573-0.5571-0.0520.44510.18950.2408-0.00850.03960.23080.09320.3786-7.1474-1.3985-6.6633
77.71651.08762.89062.32692.85943.81430.2637-0.0884-0.293-0.0425-0.0454-0.45660.2695-0.0008-0.17820.2010.0019-0.0240.21850.02230.3992-4.6748-4.02083.0471
87.29281.45332.89996.31571.96297.7361-0.0114-0.1640.6430.0992-0.0709-0.37840.05760.30480.20220.20040.0189-0.0120.1696-0.01320.4317-6.78792.32147.6272
95.34245.39386.78115.66936.52859.0396-0.66940.30021.45960.81190.04630.6124-0.6289-0.13590.59380.31240.0835-0.03550.29870.05260.5842-16.78576.08971.0387
103.14130.30990.41933.88611.61233.8092-0.50971.19910.2888-1.25270.5016-0.1731-0.29610.10210.09690.83020.04080.47550.72820.53750.469-0.8582-10.9133-26.8664
111.2786-0.09661.66820.52440.72343.5689-0.1390.78180.3132-1.1523-0.28990.0444-0.45410.39280.28940.79030.30340.04430.57890.32980.3408-9.4232-7.7809-23.914
125.0118-0.51324.4062.4887-1.43934.2812-0.11461.3420.2284-1.0433-0.2858-0.5165-0.16340.54580.42640.65890.21040.16260.62540.12880.2533-2.7614-19.8494-24.7034
130.3503-0.532-0.26253.2358-0.50452.70580.22940.4170.0514-0.8699-0.26240.5479-0.1376-0.45290.03390.39260.1296-0.14930.37820.00980.3023-14.4319-21.3577-19.9337
148.78740.32930.68083.5807-3.68296.5177-0.0705-0.0537-0.3207-0.7828-0.09891.19850.4838-1.37820.1630.4012-0.0842-0.14980.4131-0.18330.6859-23.7635-33.9467-15.4771
156.45454.2951.44373.7909-0.26391.98580.64340.2556-0.3638-0.4246-0.6860.35750.4035-0.4456-0.00330.38850.0674-0.11210.4658-0.19940.4189-12.2902-36.7793-17.2846
169.63523.4693.07946.9657-1.79496.4487-0.06340.4201-0.5358-0.5906-0.24751.14461.118-0.9808-0.04420.5046-0.0577-0.04970.4214-0.32270.4898-15.5664-40.9784-21.1614
174.979-0.3662-4.67482.5964-1.26055.3977-0.01440.8893-1.6047-0.14090.1109-1.06271.4943-0.15570.02220.98120.1599-0.26040.5881-0.33870.785-8.86-41.8719-27.0568
181.28280.92531.22970.68150.9711.73620.14880.3394-0.2233-0.18540.01990.12760.331-0.7245-0.27590.87890.2009-0.56520.7333-0.22650.3458-16.1837-33.1041-31.9972
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 186:201)A186 - 201
2X-RAY DIFFRACTION2chain 'A' and (resseq 202:220)A202 - 220
3X-RAY DIFFRACTION3chain 'A' and (resseq 221:240)A221 - 240
4X-RAY DIFFRACTION4chain 'A' and (resseq 241:263)A241 - 263
5X-RAY DIFFRACTION5chain 'A' and (resseq 264:274)A264 - 274
6X-RAY DIFFRACTION6chain 'A' and (resseq 275:321)A275 - 321
7X-RAY DIFFRACTION7chain 'A' and (resseq 322:351)A322 - 351
8X-RAY DIFFRACTION8chain 'A' and (resseq 352:386)A352 - 386
9X-RAY DIFFRACTION9chain 'A' and (resseq 387:398)A387 - 398
10X-RAY DIFFRACTION10chain 'B' and (resseq 186:201)B186 - 201
11X-RAY DIFFRACTION11chain 'B' and (resseq 202:220)B202 - 220
12X-RAY DIFFRACTION12chain 'B' and (resseq 221:240)B221 - 240
13X-RAY DIFFRACTION13chain 'B' and (resseq 241:300)B241 - 300
14X-RAY DIFFRACTION14chain 'B' and (resseq 301:322)B301 - 322
15X-RAY DIFFRACTION15chain 'B' and (resseq 323:352)B323 - 352
16X-RAY DIFFRACTION16chain 'B' and (resseq 353:369)B353 - 369
17X-RAY DIFFRACTION17chain 'B' and (resseq 370:386)B370 - 386
18X-RAY DIFFRACTION18chain 'B' and (resseq 387:398)B387 - 398

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