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- PDB-4n8x: The structure of Nostoc sp. PCC 7120 CcmL -

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Basic information

Entry
Database: PDB / ID: 4n8x
TitleThe structure of Nostoc sp. PCC 7120 CcmL
ComponentsCarbon dioxide concentrating mechanism protein
KeywordsSTRUCTURAL PROTEIN / CcmL / stranded beta barrel / bacterial microcompartment vertex protein / carboxysome
Function / homologyEutN/Ccml / Bacterial microcompartment vertex (BMV) domain profile. / Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL / EutN/Ccml superfamily / Ethanolamine utilisation protein EutN/carboxysome / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta / Carboxysome vertex protein CcmL
Function and homology information
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsKeeling, T.J. / Kimber, M.S.
CitationJournal: Photosynth.Res. / Year: 2014
Title: Interactions and structural variability of beta-carboxysomal shell protein CcmL.
Authors: Keeling, T.J. / Samborska, B. / Demers, R.W. / Kimber, M.S.
History
DepositionOct 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Sep 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
1: Carbon dioxide concentrating mechanism protein
2: Carbon dioxide concentrating mechanism protein
3: Carbon dioxide concentrating mechanism protein
4: Carbon dioxide concentrating mechanism protein
A: Carbon dioxide concentrating mechanism protein
B: Carbon dioxide concentrating mechanism protein
C: Carbon dioxide concentrating mechanism protein
D: Carbon dioxide concentrating mechanism protein
E: Carbon dioxide concentrating mechanism protein
F: Carbon dioxide concentrating mechanism protein
G: Carbon dioxide concentrating mechanism protein
H: Carbon dioxide concentrating mechanism protein
I: Carbon dioxide concentrating mechanism protein
J: Carbon dioxide concentrating mechanism protein
K: Carbon dioxide concentrating mechanism protein
L: Carbon dioxide concentrating mechanism protein
M: Carbon dioxide concentrating mechanism protein
N: Carbon dioxide concentrating mechanism protein
O: Carbon dioxide concentrating mechanism protein
P: Carbon dioxide concentrating mechanism protein
Q: Carbon dioxide concentrating mechanism protein
R: Carbon dioxide concentrating mechanism protein
S: Carbon dioxide concentrating mechanism protein
T: Carbon dioxide concentrating mechanism protein
U: Carbon dioxide concentrating mechanism protein
V: Carbon dioxide concentrating mechanism protein
W: Carbon dioxide concentrating mechanism protein
X: Carbon dioxide concentrating mechanism protein
Y: Carbon dioxide concentrating mechanism protein
Z: Carbon dioxide concentrating mechanism protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)368,40431
Polymers368,30830
Non-polymers961
Water31,5261750
1
1: Carbon dioxide concentrating mechanism protein
2: Carbon dioxide concentrating mechanism protein
3: Carbon dioxide concentrating mechanism protein
4: Carbon dioxide concentrating mechanism protein
Z: Carbon dioxide concentrating mechanism protein


Theoretical massNumber of molelcules
Total (without water)61,3855
Polymers61,3855
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11430 Å2
ΔGint-41 kcal/mol
Surface area19590 Å2
MethodPISA
2
A: Carbon dioxide concentrating mechanism protein
B: Carbon dioxide concentrating mechanism protein
C: Carbon dioxide concentrating mechanism protein
D: Carbon dioxide concentrating mechanism protein
E: Carbon dioxide concentrating mechanism protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4816
Polymers61,3855
Non-polymers961
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11930 Å2
ΔGint-58 kcal/mol
Surface area20130 Å2
MethodPISA
3
F: Carbon dioxide concentrating mechanism protein
G: Carbon dioxide concentrating mechanism protein
H: Carbon dioxide concentrating mechanism protein
I: Carbon dioxide concentrating mechanism protein
J: Carbon dioxide concentrating mechanism protein


Theoretical massNumber of molelcules
Total (without water)61,3855
Polymers61,3855
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11620 Å2
ΔGint-43 kcal/mol
Surface area19640 Å2
MethodPISA
4
K: Carbon dioxide concentrating mechanism protein
L: Carbon dioxide concentrating mechanism protein
M: Carbon dioxide concentrating mechanism protein
N: Carbon dioxide concentrating mechanism protein
O: Carbon dioxide concentrating mechanism protein


Theoretical massNumber of molelcules
Total (without water)61,3855
Polymers61,3855
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11720 Å2
ΔGint-40 kcal/mol
Surface area19540 Å2
MethodPISA
5
P: Carbon dioxide concentrating mechanism protein
Q: Carbon dioxide concentrating mechanism protein
R: Carbon dioxide concentrating mechanism protein
S: Carbon dioxide concentrating mechanism protein
T: Carbon dioxide concentrating mechanism protein


Theoretical massNumber of molelcules
Total (without water)61,3855
Polymers61,3855
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11530 Å2
ΔGint-43 kcal/mol
Surface area19560 Å2
MethodPISA
6
U: Carbon dioxide concentrating mechanism protein
V: Carbon dioxide concentrating mechanism protein
W: Carbon dioxide concentrating mechanism protein
X: Carbon dioxide concentrating mechanism protein
Y: Carbon dioxide concentrating mechanism protein


Theoretical massNumber of molelcules
Total (without water)61,3855
Polymers61,3855
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11350 Å2
ΔGint-46 kcal/mol
Surface area19940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.880, 128.120, 220.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ...
Carbon dioxide concentrating mechanism protein


Mass: 12276.924 Da / Num. of mol.: 30
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / UTEX 2576 / Gene: ccmL / Plasmid: PET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8YYI2
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1750 / 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: 2.26 Å3/Da / Density % sol: 45.59 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 4.4
Details: 0.1 M Na acetate, 20 % (vol/vol) PEG 8000, 0.1 M Li2SO4, 1 % ethylene glycol, pH 4.4, VAPOR DIFFUSION, SITTING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.03322 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 12, 2012
RadiationMonochromator: WHITE BEAM SLITS, CRYO-COOLED FIRST AND SAGITTALLY BENT SECOND CRYSTAL OF DOUBLE CRYSTAL MONOCHROMATOR (DCM), VERTICALLY FOCUSING MIRROR (VFM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03322 Å / Relative weight: 1
ReflectionResolution: 1.93→48.292 Å / Num. all: 234801 / Num. obs: 234801 / % possible obs: 94 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 14.6 Å2 / Rsym value: 0.064 / Net I/σ(I): 16.6
Reflection shellResolution: 1.93→1.98 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.629 / % possible all: 65.1

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Processing

Software
NameVersionClassification
MxDCdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4N8F

4n8f


Resolution: 1.93→48.292 Å / SU ML: 0.22 / Isotropic thermal model: isotropic + TLS / σ(F): 1.99 / Phase error: 23.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2474 11569 5 %
Rwork0.2056 --
obs0.2077 231564 92.7 %
all-231566 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→48.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22551 0 5 1750 24306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01222775
X-RAY DIFFRACTIONf_angle_d1.48630788
X-RAY DIFFRACTIONf_dihedral_angle_d15.9918572
X-RAY DIFFRACTIONf_chiral_restr0.1013709
X-RAY DIFFRACTIONf_plane_restr0.0053970
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.95190.35362490.33724766X-RAY DIFFRACTION61
1.9519-1.97490.31532800.26435308X-RAY DIFFRACTION68
1.9749-1.99890.29773020.23515750X-RAY DIFFRACTION73
1.9989-2.02430.27033250.22366173X-RAY DIFFRACTION79
2.0243-2.05090.27593510.21666656X-RAY DIFFRACTION85
2.0509-2.0790.26673840.21127309X-RAY DIFFRACTION93
2.079-2.10870.26924100.2157783X-RAY DIFFRACTION99
2.1087-2.14020.26224100.21427797X-RAY DIFFRACTION99
2.1402-2.17360.26344110.20527805X-RAY DIFFRACTION99
2.1736-2.20920.26784090.23787776X-RAY DIFFRACTION99
2.2092-2.24730.4312680.34155092X-RAY DIFFRACTION80
2.2473-2.28820.39473000.29765713X-RAY DIFFRACTION83
2.2882-2.33220.25424100.19227790X-RAY DIFFRACTION99
2.3322-2.37980.22124140.18287866X-RAY DIFFRACTION100
2.3798-2.43160.23134100.18457803X-RAY DIFFRACTION100
2.4316-2.48810.22974140.19557858X-RAY DIFFRACTION100
2.4881-2.55030.25514140.19557872X-RAY DIFFRACTION100
2.5503-2.61930.24234140.20187858X-RAY DIFFRACTION100
2.6193-2.69640.24624140.19537870X-RAY DIFFRACTION100
2.6964-2.78340.23864150.1977883X-RAY DIFFRACTION100
2.7834-2.88280.23384150.19247890X-RAY DIFFRACTION100
2.8828-2.99830.24034170.19727912X-RAY DIFFRACTION100
2.9983-3.13470.25784150.20527904X-RAY DIFFRACTION100
3.1347-3.29990.22864170.20347916X-RAY DIFFRACTION100
3.2999-3.50660.22064170.18887927X-RAY DIFFRACTION100
3.5066-3.77730.27583970.2477706X-RAY DIFFRACTION96
3.7773-4.15720.23124150.18377874X-RAY DIFFRACTION99
4.1572-4.75830.19914210.16478005X-RAY DIFFRACTION100
4.7583-5.99320.22454230.18218040X-RAY DIFFRACTION99
5.9932-48.30730.24654280.22418093X-RAY DIFFRACTION97
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)
13.1985-2.3303-0.39233.73240.39652.3373-0.0848-0.3920.25580.13520.1598-0.348-0.31950.3087-0.06180.1877-0.07210.03030.2579-0.03110.193719.5787-37.1195-7.8058
23.29520.4365-0.39542.1490.28092.97150.02120.07930.1164-0.1209-0.02930.0942-0.2703-0.1028-0.01370.18770.01560.02290.12010.01620.09452.4079-34.3076-18.2364
31.7703-0.614-1.0242.82890.03472.6729-0.09530.1391-0.2928-0.0653-0.02460.35840.2728-0.37870.06890.232-0.03160.00060.2716-0.05060.1432-4.6543-52.5873-23.8931
43.47360.07730.52352.967-1.37853.8809-0.0877-0.1163-0.62620.0187-0.0488-0.04820.6354-0.12330.08110.3297-0.00880.12290.2324-0.01880.29438.1493-66.8239-16.4177
52.9336-0.5339-0.88624.10221.52383.9896-0.0876-0.6512-0.04630.4805-0.0142-0.11970.13550.35440.04760.18150.03580.04890.31030.01240.213922.6936-57.2046-6.7632
64.1081-0.89030.87872.1199-0.49014.1486-0.01160.6387-0.0724-0.6512-0.0732-0.21850.0822-0.0750.05870.4362-0.11530.09950.2578-0.03190.2550.2356-30.5343-77.7135
72.70890.1391-0.3954.75610.56953.2738-0.08660.35340.4851-0.29820.10690.1475-0.2732-0.1946-0.01270.1807-0.0979-0.01960.29660.04850.255136.0203-17.0769-73.9308
83.93431.60292.30282.47120.80712.9628-0.1774-0.07120.38190.2066-0.0710.3634-0.2617-0.35710.2290.18740.00730.06540.2205-0.01160.232139.6311-8.4708-55.6696
93.2857-0.158-0.4243.28340.23112.8078-0.0096-0.2146-0.06610.2849-0.0544-0.16680.04950.13460.04770.1773-0.02620.01360.10880.01820.102956.494-16.6854-48.3153
102.29060.32540.93562.6082-0.08032.5926-0.14930.336-0.2672-0.3151-0.0273-0.5720.27970.4040.14270.29210.00390.1020.17780.02190.306862.8602-30.2428-61.5776
114.11221.02860.3924.3308-0.67162.6513-0.211-0.5573-0.51370.51380.206-0.1740.38290.2907-0.00120.46630.1210.07770.32980.01330.235754.395-67.8054-16.2306
122.54460.01970.04413.01920.3043.1377-0.13080.2888-0.5520.1141-0.0380.23720.4458-0.1380.11840.2377-0.00760.14390.1986-0.06810.330338.7045-73.1181-27.8376
131.73620.865-2.651.7809-0.81174.1017-0.06030.5025-0.0651-0.26580.0540.183-0.006-0.7690.02180.18670.0371-0.00070.3053-0.03520.257639.1178-61.3581-44.8635
143.1553-0.1030.05192.64520.4993.4654-0.0274-0.020.1228-0.15710.0397-0.0507-0.31850.1560.01780.21560.00410.0280.07670.01080.108155.4488-49.56-43.6455
151.64790.002-0.28582.9855-0.48372.9997-0.0147-0.2537-0.08060.40460.0755-0.3389-0.01750.5121-0.01910.28330.0197-0.04170.2206-0.06660.205264.5583-53.178-26.4395
164.27-0.1221-1.04023.04940.99371.9553-0.0729-0.17710.5334-0.0213-0.045-0.1168-0.96470.12880.02920.4951-0.0254-0.11110.23330.04910.270954.21044.1335-15.0984
173.1537-0.3115-0.3423.2588-0.76033.5494-0.1746-0.33730.17120.34270.0580.13-0.3621-0.24850.08450.21490.0713-0.05830.2351-0.04540.183938.6083-4.0295-5.6063
182.3215-1.98860.49763.6573-1.14411.8941-0.0307-0.242-0.258-0.12880.17650.42840.2962-0.3896-0.11520.1611-0.0702-0.01950.27760.00240.184239.4549-24.5303-7.2267
193.21470.59530.15882.0165-0.13773.0077-0.0660.048-0.0077-0.1139-0.0059-0.11050.23060.05550.04090.15290.0055-0.01760.0821-0.01170.108756.0542-28.9482-17.6955
201.5835-0.61870.05053.4837-0.30722.7904-0.07950.10870.1961-0.0419-0.0435-0.4127-0.33020.56140.05120.177-0.0642-0.01420.27010.0150.1564.9755-12.633-23.0421
211.84520.36091.44121.7824-0.40562.96710.14190.5434-0.0023-0.4129-0.131-0.24770.47950.6129-0.02990.3030.16360.01470.33040.00560.203118.5411-4.4055-46.4909
222.7818-0.7154-0.41782.8093-0.54643.40420.1590.1587-0.2262-0.36360.06670.32280.5088-0.1817-0.21090.39960.0451-0.13490.1626-0.00330.21181.0009-13.8522-43.4247
232.2340.14560.57642.26050.09313.3002-0.0318-0.29790.08290.11420.22610.5324-0.0054-0.646-0.12450.25110.04480.02060.32250.12610.2807-5.165-8.7296-24.8353
244.56161.7335-0.55114.36460.87242.5196-0.0846-0.35190.56270.45160.13590.3173-0.3421-0.0465-0.03480.36170.1268-0.02030.2945-0.00340.18398.47394.0328-16.321
252.4213-0.06530.52893.4269-0.79525.0038-0.14460.20540.3693-0.21660.0802-0.0754-0.35130.12030.03890.19660.0387-0.07140.21340.0030.224222.77766.785-29.9331
261.70821.1347-1.85733.2066-0.94233.4068-0.1031-0.0199-0.33770.1515-0.0269-0.46750.06480.38390.12130.1691-0.026-0.06440.2944-0.00980.259619.703-52.4314-58.7114
273.0032-0.22130.87383.072-0.08822.9226-0.1178-0.07520.07310.17440.09320.1173-0.1282-0.02470.01320.187-0.0412-0.01160.1232-0.01140.08732.8197-46.432-49.2198
281.64540.2708-0.59282.7372-0.252.9741-0.08550.21450.2654-0.4007-0.04430.4572-0.4573-0.30340.08250.32560.0264-0.09990.1788-0.02420.2979-6.8025-33.6329-61.3002
294.516-0.9365-0.80772.54230.62144.008-0.10970.6690.0101-0.5716-0.13640.2799-0.4147-0.11390.18820.4833-0.0961-0.11790.27760.04210.29143.3103-31.6956-79.012
303.10050.39570.26154.5206-0.08992.6966-0.12260.5674-0.4018-0.52340.2295-0.21080.00690.2963-0.14560.2702-0.1540.02940.3711-0.08060.266119.7433-43.4997-77.3481
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H
9X-RAY DIFFRACTION9CHAIN I
10X-RAY DIFFRACTION10CHAIN J
11X-RAY DIFFRACTION11CHAIN K
12X-RAY DIFFRACTION12CHAIN L
13X-RAY DIFFRACTION13CHAIN M
14X-RAY DIFFRACTION14CHAIN N
15X-RAY DIFFRACTION15CHAIN O
16X-RAY DIFFRACTION16CHAIN P
17X-RAY DIFFRACTION17CHAIN Q
18X-RAY DIFFRACTION18CHAIN R
19X-RAY DIFFRACTION19CHAIN S
20X-RAY DIFFRACTION20CHAIN T
21X-RAY DIFFRACTION21CHAIN U
22X-RAY DIFFRACTION22CHAIN V
23X-RAY DIFFRACTION23CHAIN W
24X-RAY DIFFRACTION24CHAIN X
25X-RAY DIFFRACTION25CHAIN Y
26X-RAY DIFFRACTION26CHAIN Z
27X-RAY DIFFRACTION27CHAIN 1
28X-RAY DIFFRACTION28CHAIN 2
29X-RAY DIFFRACTION29CHAIN 3
30X-RAY DIFFRACTION30CHAIN 4

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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