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- PDB-3pcq: Femtosecond X-ray protein Nanocrystallography -

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Basic information

Entry
Database: PDB / ID: 3pcq
TitleFemtosecond X-ray protein Nanocrystallography
Components(Photosystem I ...) x 12
KeywordsPHOTOSYNTHESIS / MEMBRANE PROTEIN / MULTIPROTEIN-PIGMENT COMPLEX
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / : / electron transfer activity ...photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / : / electron transfer activity / magnesium ion binding / integral component of membrane / metal ion binding
Similarity search - Function
Photosystem I PsaX / PsaX family / Photosystem I PsaX superfamily / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction centre subunit PsaK superfamily ...Photosystem I PsaX / PsaX family / Photosystem I PsaX superfamily / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I reaction centre subunit III / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaD / PsaD / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaE, reaction centre subunit IV / Photosystem I protein PsaC / Photosystem I PsaB / Photosystem I psaA and psaB proteins signature. / Photosystem I PsaA/PsaB, conserved site / Photosystem I PsaA / Photosystem I psaA/psaB protein / Photosystem I PsaA/PsaB superfamily / Photosystem I PsaA/PsaB / Electron transport accessory-like domain superfamily / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit II / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit PsaK / Photosystem I reaction center subunit IV / Photosystem I iron-sulfur center / BETA-CAROTENE / Photosystem I P700 chlorophyll a apoprotein A1 ...Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit II / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit PsaK / Photosystem I reaction center subunit IV / Photosystem I iron-sulfur center / BETA-CAROTENE / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit XII / Photosystem I reaction center subunit III / CHLOROPHYLL A / IRON/SULFUR CLUSTER / PHYLLOQUINONE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Photosystem I 4.8K protein
Similarity search - Component
Biological speciesThermosynechococcus elongatus (Cyanobacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 8.984 Å
AuthorsChapman, H.N. / Fromme, P. / Barty, A. / White, T.A. / Kirian, R.A. / Aquila, A. / Hunter, M.S. / Schulz, J. / Deponte, D.P. / Weierstall, U. ...Chapman, H.N. / Fromme, P. / Barty, A. / White, T.A. / Kirian, R.A. / Aquila, A. / Hunter, M.S. / Schulz, J. / Deponte, D.P. / Weierstall, U. / Doak, R.B. / Maia, F.R.N.C. / Martin, A.V. / Schlichting, I. / Lomb, L. / Coppola, N. / Shoeman, R.L. / Epp, S.W. / Hartmann, R. / Rolles, D. / Rudenko, A. / Foucar, L. / Kimmel, N. / Weidenspointner, G. / Holl, P. / Liang, M. / Barthelmess, M. / Caleman, C. / Boutet, S. / Bogan, M.J. / Krzywinski, J. / Bostedt, C. / Bajt, S. / Gumprecht, L. / Rudek, B. / Erk, B. / Schmidt, C. / Homke, A. / Reich, C. / Pietschner, D. / Struder, L. / Hauser, G. / Gorke, H. / Ullrich, J. / Herrmann, S. / Schaller, G. / Schopper, F. / Soltau, H. / Kuhnel, K.-U. / Messerschmidt, M. / Bozek, J.D. / Hau-Riege, S.P. / Frank, M. / Hampton, C.Y. / Sierra, R. / Starodub, D. / Williams, G.J. / Hajdu, J. / Timneanu, N. / Seibert, M.M. / Andreasson, J. / Rocker, A. / Jonsson, O. / Svenda, M. / Stern, S. / Nass, K. / Andritschke, R. / Schroter, C.-D. / Krasniqi, F. / Bott, M. / Schmidt, K.E. / Wang, X. / Grotjohann, I. / Holton, J.M. / Barends, T.R.M. / Neutze, R. / Marchesini, S. / Fromme, R. / Schorb, S. / Rupp, D. / Adolph, M. / Gorkhover, T. / Andersson, I. / Hirsemann, H. / Potdevin, G. / Graafsma, H. / Nilsson, B. / Spence, J.C.H.
Citation
Journal: Nature / Year: 2011
Title: Femtosecond X-ray protein nanocrystallography.
Authors: Chapman, H.N. / Fromme, P. / Barty, A. / White, T.A. / Kirian, R.A. / Aquila, A. / Hunter, M.S. / Schulz, J. / Deponte, D.P. / Weierstall, U. / Doak, R.B. / Maia, F.R. / Martin, A.V. / ...Authors: Chapman, H.N. / Fromme, P. / Barty, A. / White, T.A. / Kirian, R.A. / Aquila, A. / Hunter, M.S. / Schulz, J. / Deponte, D.P. / Weierstall, U. / Doak, R.B. / Maia, F.R. / Martin, A.V. / Schlichting, I. / Lomb, L. / Coppola, N. / Shoeman, R.L. / Epp, S.W. / Hartmann, R. / Rolles, D. / Rudenko, A. / Foucar, L. / Kimmel, N. / Weidenspointner, G. / Holl, P. / Liang, M. / Barthelmess, M. / Caleman, C. / Boutet, S. / Bogan, M.J. / Krzywinski, J. / Bostedt, C. / Bajt, S. / Gumprecht, L. / Rudek, B. / Erk, B. / Schmidt, C. / Homke, A. / Reich, C. / Pietschner, D. / Struder, L. / Hauser, G. / Gorke, H. / Ullrich, J. / Herrmann, S. / Schaller, G. / Schopper, F. / Soltau, H. / Kuhnel, K.U. / Messerschmidt, M. / Bozek, J.D. / Hau-Riege, S.P. / Frank, M. / Hampton, C.Y. / Sierra, R.G. / Starodub, D. / Williams, G.J. / Hajdu, J. / Timneanu, N. / Seibert, M.M. / Andreasson, J. / Rocker, A. / Jonsson, O. / Svenda, M. / Stern, S. / Nass, K. / Andritschke, R. / Schroter, C.D. / Krasniqi, F. / Bott, M. / Schmidt, K.E. / Wang, X. / Grotjohann, I. / Holton, J.M. / Barends, T.R. / Neutze, R. / Marchesini, S. / Fromme, R. / Schorb, S. / Rupp, D. / Adolph, M. / Gorkhover, T. / Andersson, I. / Hirsemann, H. / Potdevin, G. / Graafsma, H. / Nilsson, B. / Spence, J.C.
#1: Journal: Nature / Year: 2001
Title: Three-dimensional structure of cyanobacterial photosystem I at 2.5 A resolution
Authors: Jordan, P. / Fromme, P. / Witt, H.T. / Klukas, O. / Saenger, W. / Krauss, N.
History
DepositionOct 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 8, 2012Group: Data collection
Revision 1.3Jul 25, 2012Group: Non-polymer description
Revision 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Feb 14, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_site / _diffrn_source.source / _diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II
E: Photosystem I reaction center subunit IV
F: Photosystem I reaction center subunit III
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit PsaK
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
X: Photosystem I 4.8K protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)359,828140
Polymers257,29012
Non-polymers102,539128
Water3,603200
1
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II
E: Photosystem I reaction center subunit IV
F: Photosystem I reaction center subunit III
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit PsaK
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
X: Photosystem I 4.8K protein
hetero molecules

A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II
E: Photosystem I reaction center subunit IV
F: Photosystem I reaction center subunit III
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit PsaK
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
X: Photosystem I 4.8K protein
hetero molecules

A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II
E: Photosystem I reaction center subunit IV
F: Photosystem I reaction center subunit III
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit PsaK
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
X: Photosystem I 4.8K protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,079,485420
Polymers771,86936
Non-polymers307,616384
Water54030
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area178410 Å2
ΔGint-1363 kcal/mol
Surface area298530 Å2
Unit cell
Length a, b, c (Å)281.000, 281.000, 165.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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Photosystem I ... , 12 types, 12 molecules ABCDEFIJKLMX

#1: Protein Photosystem I P700 chlorophyll a apoprotein A1 / / PsaA


Mass: 83267.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: P0A405
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / / PsaB


Mass: 82992.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: P0A407
#3: Protein Photosystem I iron-sulfur center / / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8678.011 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: P0A415
#4: Protein Photosystem I reaction center subunit II / / Photosystem I 16 kDa polypeptide / PSI-D


Mass: 15258.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: P0A420
#5: Protein Photosystem I reaction center subunit IV / / Photosystem I 8.1 kDa protein / p30 protein


Mass: 8268.290 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: P0A423
#6: Protein Photosystem I reaction center subunit III / / PSI-F


Mass: 17716.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: P0A401
#7: Protein/peptide Photosystem I reaction center subunit VIII /


Mass: 4297.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: P0A427
#8: Protein/peptide Photosystem I reaction center subunit IX /


Mass: 4770.698 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: P0A429
#9: Protein Photosystem I reaction center subunit PsaK / / Light-harvesting 8.0 kDa polypeptide / Photosystem I subunit X


Mass: 8483.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: P0A425
#10: Protein Photosystem I reaction center subunit XI / / PSI subunit V / PSI-L


Mass: 16156.569 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: Q8DGB4
#11: Protein/peptide Photosystem I reaction center subunit XII / / PSI-M


Mass: 3426.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: P0A403
#12: Protein/peptide Photosystem I 4.8K protein /


Mass: 3973.744 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: Q8DKP6

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Non-polymers , 8 types, 328 molecules

#13: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 96 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#14: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE / Phytomenadione


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2
#15: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#16: Chemical...
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C40H56
#17: Chemical ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#18: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H86O10
#19: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#20: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 15445

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Sample preparation

Crystal growTemperature: 277 K / pH: 6.4
Details: 0.008 M MAGNESIUM SULFATE, 0.005 M MES PH 6.4, 0.02% BETA-DODECYLMALTOSIDE, Batch nanocrystallization, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12881
21001
Diffraction source
SourceSiteBeamlineIDWavelength
FREE ELECTRON LASERSLAC LCLS AMO16.9
SYNCHROTRONALS 8.2.221
Detector
TypeIDDetectorDateDetails
CFEL-ASG MULTIPURPOSE (CAMP)1PNCCDDec 13, 2009KB MIRRORS
ADSC QUANTUM 315r2CCDJul 16, 2010
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1SI 111
Radiation wavelength
IDWavelength (Å)Relative weight
16.91
211
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.5
11K, H, -L20.5
ReflectionResolution: 8.66→243.47 Å / Num. all: 6677 / Num. obs: 6111 / % possible obs: 91.52 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 738 % / Net I/σ(I): 11.11
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allDiffraction-ID% possible all
8.66-9112.754741,270.5
9-9.86123.43.081613391,2100
9.86-11.02496.27.6887512141,2100
11.02-12.73937.913.208410671,2100
12.73-15.591265.512.7369101,2100
15.59-22.051407.216.24067061,2100
22.05-831480.214.24474011,298

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Processing

Software
NameVersionClassification
LCLSDAQdata collection
CASSdata collection
IDL(IN HOUSE)data collection
REFMAC5.6.0076refinement
CrystFEL0.1.0 / indexamajig (IN HOUSE)data reduction
MonteCarlo Integration (IN HOUSE)data scaling
REFMAC5.6.0076phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JB0
Resolution: 8.984→81.12 Å / Cor.coef. Fo:Fc: 0.777 / Cor.coef. Fo:Fc free: 0.758 / SU B: 571.44 / SU ML: 3.653 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.973 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 187 3.3 %RANDOM
Rwork0.25185 ---
obs0.25118 5404 98.5 %-
all-6677 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.257 Å2
Baniso -1Baniso -2Baniso -3
1-36.87 Å20 Å20 Å2
2--36.87 Å20 Å2
3----73.73 Å2
Refinement stepCycle: LAST / Resolution: 8.984→81.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17393 0 6603 200 24196
LS refinement shellResolution: 8.984→9.217 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.128 8 -
Rwork0.275 379 -
obs-430 90.42 %

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