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- PDB-4lm6: Light harvesting complex PC612 from the cryptophyte Hemiselmis vi... -

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Basic information

Entry
Database: PDB / ID: 4lm6
TitleLight harvesting complex PC612 from the cryptophyte Hemiselmis virescens M1635
Components
  • cryptophyte phycocyanin alpha chain
  • cryptophyte phycocyanin beta chain
KeywordsPHOTOSYNTHESIS / phycobiliprotein / thylakoid lumen
Function / homology
Function and homology information


: / : / phycobilisome / chloroplast thylakoid membrane / photosynthesis
Similarity search - Function
Cryptophytan Phycoerythrin (Alpha-1 Chain); Chain A / Phycoerythrin alpha chain / Phycoerythrin alpha chain / Phycoerythrin-like alpha chain superfamily / Phycoerythrin, alpha/beta chain / Phycocyanins / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globular protein, non-globular alpha/beta subunit ...Cryptophytan Phycoerythrin (Alpha-1 Chain); Chain A / Phycoerythrin alpha chain / Phycoerythrin alpha chain / Phycoerythrin-like alpha chain superfamily / Phycoerythrin, alpha/beta chain / Phycocyanins / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globular protein, non-globular alpha/beta subunit / Globin-like / Globin-like superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHYCOCYANOBILIN / 15,16-DIHYDROBILIVERDIN / Cryptophyte phycocyanin alpha chain / Phycoerythrin beta subunit
Similarity search - Component
Biological speciesHemiselmis virescens (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHarrop, S.J. / Wilk, K.E. / Curmi, P.M.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Single-residue insertion switches the quaternary structure and exciton states of cryptophyte light-harvesting proteins.
Authors: Harrop, S.J. / Wilk, K.E. / Dinshaw, R. / Collini, E. / Mirkovic, T. / Teng, C.Y. / Oblinsky, D.G. / Green, B.R. / Hoef-Emden, K. / Hiller, R.G. / Scholes, G.D. / Curmi, P.M.
History
DepositionJul 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cryptophyte phycocyanin alpha chain
B: cryptophyte phycocyanin beta chain
C: cryptophyte phycocyanin alpha chain
D: cryptophyte phycocyanin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,20812
Polymers49,5074
Non-polymers4,7018
Water12,124673
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19530 Å2
ΔGint-187 kcal/mol
Surface area19820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.081, 132.081, 64.362
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein cryptophyte phycocyanin alpha chain


Mass: 6525.596 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Hemiselmis virescens (eukaryote) / Strain: M1635 / References: UniProt: A0A075B5G1*PLUS
#2: Protein cryptophyte phycocyanin beta chain


Mass: 18227.732 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Hemiselmis virescens (eukaryote) / Strain: M1635 / References: UniProt: A0A075B5G2*PLUS
#3: Chemical
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Chemical ChemComp-DBV / 15,16-DIHYDROBILIVERDIN


Mass: 584.662 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H36N4O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 673 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.27 Å3/Da / Density % sol: 62.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG3350, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 29, 2010
RadiationMonochromator: double crystal Si(111) with sagittally bent second crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.7→38.13 Å / Num. all: 70449 / Num. obs: 70433 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.3 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 24
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 3.3 / Num. unique all: 10054 / Rsym value: 0.79 / % possible all: 98

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Processing

Software
NameVersionClassification
Blu-IceICEdata collection
PHASERphasing
PHENIX(phenix.refine: dev_1415)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QGW, CHAIN C

1qgw


Resolution: 1.7→28.929 Å / SU ML: 0.17 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 19.44 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.197 3565 5.06 %RANDOM
Rwork0.161 ---
all0.1629 70433 --
obs0.1629 70433 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→28.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3428 0 344 673 4445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013928
X-RAY DIFFRACTIONf_angle_d1.3165340
X-RAY DIFFRACTIONf_dihedral_angle_d16.2241439
X-RAY DIFFRACTIONf_chiral_restr0.067574
X-RAY DIFFRACTIONf_plane_restr0.006687
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.7-1.72330.31351580.257326552655
1.7233-1.74790.24581340.232926622662
1.7479-1.7740.1911300.216226752675
1.774-1.80170.25261250.212726382638
1.8017-1.83120.25761530.215926842684
1.8312-1.86280.27441480.217626622662
1.8628-1.89670.28981380.215526092609
1.8967-1.93320.24811620.203326802680
1.9332-1.97260.23081310.195326612661
1.9726-2.01550.22131450.188426652665
2.0155-2.06240.22811340.18126742674
2.0624-2.11390.1851280.177326592659
2.1139-2.17110.20141610.172426722672
2.1711-2.23490.21771380.171726612661
2.2349-2.3070.2311240.16826992699
2.307-2.38940.23671430.164326662666
2.3894-2.48510.23941460.159626762676
2.4851-2.59810.16461580.152726652665
2.5981-2.7350.21581330.152726692669
2.735-2.90620.18961080.160827112711
2.9062-3.13030.19731620.154726852685
3.1303-3.44490.1781650.148226612661
3.4449-3.94230.15861430.137926962696
3.9423-4.96280.15291480.121427172717
4.9628-28.93340.16541500.137427662766
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)
11.59751.66020.52253.99220.28251.13080.02180.3762-0.1579-0.1648-0.1242-0.0895-0.1740.0679-0.02270.1366-0.00840.06470.2732-0.12420.2575-39.532816.063-15.461
22.097-1.04650.58851.93672.95377.6304-0.00750.37130.3878-0.30770.1909-0.4332-0.34660.5488-0.14630.2679-0.05160.07370.4374-0.02620.4783-23.653921.6977-13.819
33.0667-0.2836-1.01852.00060.07392.08290.00550.344-0.1415-0.2158-0.0719-0.2206-0.13070.19540.11010.1467-0.02440.02730.274-0.05270.1941-36.781916.6875-15.0971
43.5432-4.07660.39945.99121.82735.4416-0.15050.14760.18820.1566-0.0032-0.0228-0.1435-0.07170.220.1701-0.00740.07640.13950.04730.278-59.829517.86861.3698
50.78550.52060.18235.4651-3.60553.13790.02150.9376-0.2033-1.099-0.0013-0.34210.37720.3217-0.02280.43430.00770.10190.5935-0.13110.3178-36.831410.388-26.3697
63.44093.3937-0.40375.4359-1.96633.01150.09520.4711-0.4998-0.4679-0.1772-0.65230.20940.28870.07620.22020.00370.10050.3512-0.13310.3785-32.079911.4787-18.2934
71.7119-0.4453-0.84330.51310.36230.46750.03770.36940.1102-0.39640.0852-0.1860.002-0.06760.03450.4674-0.04710.24690.85430.10190.2661-33.906524.9049-29.3059
81.3894-0.4506-0.23971.7222-0.03251.26170.05580.2962-0.0538-0.0826-0.06730.008-0.14120.11060.07130.1316-0.01020.00370.1833-0.02820.1053-51.219522.9574-13.3156
91.7555-0.5587-0.08610.2922-0.17410.7532-0.16640.0542-0.37110.06180.02920.15330.2221-0.2219-0.07630.1761-0.06920.19980.1564-0.02930.5999-67.58078.693-3.1478
101.2218-0.629-0.40081.6588-0.31362.35440.04880.3428-0.4223-0.08990.01220.2490.08890.11520.12930.1194-0.00610.00660.1993-0.12470.2219-50.965912.3402-13.7073
110.46460.1546-0.20590.9610.21610.22490.00140.3389-0.3545-0.2586-0.00710.33790.0342-0.00830.24240.2093-0.0759-0.02770.4222-0.36460.4373-55.3366.2464-22.0076
122.95932.33010.23214.14580.08161.5872-0.03330.41150.0518-0.1389-0.10010.3161-0.1413-0.06580.12190.15290.0123-0.03180.2297-0.04260.1782-57.554224.6916-15.3493
132.7752-2.19740.45382.97421.72483.60290.10680.116-0.19140.2386-0.19180.3111-0.10980.06250.04230.2256-0.0481-0.00390.2135-0.01160.1799-47.597633.2167-9.4048
142.1991.13090.41452.99720.60021.7153-0.02030.8472-0.1211-0.62090.10820.2781-0.1773-0.09480.02290.25890.0349-0.04040.4598-0.04720.2053-53.174723.4306-24.6851
152.0566-1.4638-2.23013.8287-0.47967.1946-0.2871-0.18290.24990.3402-0.0909-0.3836-0.35440.57980.31330.3940.1466-0.25680.246-0.05170.4305-24.953423.490213.6893
164.30822.77340.93643.11780.76361.21-0.1919-0.1693-0.40660.38910.2540.12510.212-0.0384-0.05080.37190.11030.06340.18290.07230.3314-46.17768.23428.6612
173.5048-3.36760.48257.18861.94912.03030.0369-0.024-0.23780.28860.0430.18020.0034-0.0644-0.06190.44510.10550.0960.18370.03850.4852-46.0014-1.85791.935
181.44771.15350.46782.6351-0.94831.1922-0.1129-0.3451-0.46820.48260.27580.04840.2167-0.05580.04140.50180.12730.0990.23650.10840.4216-40.91387.35089.8185
193.2027-3.1038-0.94256.37822.29843.5356-0.16730.16130.05150.14550.0650.1027-0.0097-0.20190.10210.1497-0.0198-0.04910.12880.02880.1728-43.829734.9291-3.8671
203.09612.0264-0.65783.3005-0.40871.39870.055-0.5343-0.65680.48610.0571-0.48120.01940.19540.24540.66420.2027-0.10280.30840.11430.4485-33.01747.175615.1365
210.1355-0.08640.12290.2362-0.06620.38150.0349-0.1119-0.06850.16870.08510.06220.0325-0.10280.00140.97540.41220.19980.49140.44690.347-46.47656.002824.1032
221.4368-0.1660.01751.0612-0.12850.8654-0.2859-0.25960.09360.37410.16730.070.23360.00730.06290.27390.0769-0.02420.14540.02490.147-45.472127.85958.6868
231.92251.29620.0418.2156-0.08580.0823-0.18910.24240.4297-0.09180.197-0.396-0.17690.3018-0.10990.2139-0.0171-0.11250.1826-0.01130.4121-31.61441.9492-0.7302
241.4035-0.18090.47741.3172-1.06171.811-0.1906-0.31190.00930.43320.2782-0.24630.10650.23390.34410.31540.1206-0.10070.1771-0.02470.1454-36.39624.76229.3391
251.1941-0.2650.14460.50150.21070.1703-0.2516-0.51180.10740.68750.2496-0.41580.1650.1289-0.00220.4240.1762-0.22120.245-0.05070.2296-36.832529.789615.9806
261.39780.1141.29050.66620.64951.7277-0.2529-0.4841-0.03830.56650.25540.19530.0414-0.12350.03930.4720.15780.03730.29610.01920.1307-50.43724.866117.0858
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 30 )
3X-RAY DIFFRACTION3chain 'A' and (resid 31 through 48 )
4X-RAY DIFFRACTION4chain 'A' and (resid 49 through 62 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 11 )
6X-RAY DIFFRACTION6chain 'B' and (resid 12 through 20 )
7X-RAY DIFFRACTION7chain 'B' and (resid 21 through 33 )
8X-RAY DIFFRACTION8chain 'B' and (resid 34 through 62 )
9X-RAY DIFFRACTION9chain 'B' and (resid 63 through 75 )
10X-RAY DIFFRACTION10chain 'B' and (resid 76 through 99 )
11X-RAY DIFFRACTION11chain 'B' and (resid 100 through 123 )
12X-RAY DIFFRACTION12chain 'B' and (resid 124 through 147 )
13X-RAY DIFFRACTION13chain 'B' and (resid 148 through 152 )
14X-RAY DIFFRACTION14chain 'B' and (resid 153 through 177 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 6 )
16X-RAY DIFFRACTION16chain 'C' and (resid 7 through 20 )
17X-RAY DIFFRACTION17chain 'C' and (resid 21 through 25 )
18X-RAY DIFFRACTION18chain 'C' and (resid 26 through 48 )
19X-RAY DIFFRACTION19chain 'C' and (resid 49 through 62 )
20X-RAY DIFFRACTION20chain 'D' and (resid 3 through 20 )
21X-RAY DIFFRACTION21chain 'D' and (resid 21 through 33 )
22X-RAY DIFFRACTION22chain 'D' and (resid 34 through 67 )
23X-RAY DIFFRACTION23chain 'D' and (resid 68 through 75 )
24X-RAY DIFFRACTION24chain 'D' and (resid 76 through 99 )
25X-RAY DIFFRACTION25chain 'D' and (resid 100 through 143 )
26X-RAY DIFFRACTION26chain 'D' and (resid 144 through 177 )

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