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- PDB-2pd0: Protein cgd2_2020 from Cryptosporidium parvum -

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Basic information

Entry
Database: PDB / ID: 2pd0
TitleProtein cgd2_2020 from Cryptosporidium parvum
ComponentsHypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Structural Genomics Consortium / SGC
Function / homologyProtein of unknown function DUF3228 / Protein of unknown function (DUF3228) / Protein of unknown function (DUF3228), domain 1 / YaeB-like fold / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsCymborowski, M. / Chruszcz, M. / Hills, T. / Lew, J. / Melone, M. / Zhao, Y. / Artz, J. / Wernimont, A. / Edwards, A. / Sundstrom, M. ...Cymborowski, M. / Chruszcz, M. / Hills, T. / Lew, J. / Melone, M. / Zhao, Y. / Artz, J. / Wernimont, A. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Arrowsmith, C. / Hui, R. / Minor, W. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Protein cgd2_2020 from Cryptosporidium parvum
Authors: Cymborowski, M. / Chruszcz, M. / Hills, T. / Lew, J. / Melone, M. / Zhao, Y. / Artz, J. / Wernimont, A. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Arrowsmith, C. / Hui, R. / Minor, W.
History
DepositionMar 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Hypothetical protein
B: Hypothetical protein
C: Hypothetical protein
D: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,7458
Polymers103,9644
Non-polymers7814
Water7,710428
1
A: Hypothetical protein
C: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3734
Polymers51,9822
Non-polymers3902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint2 kcal/mol
Surface area19630 Å2
MethodPISA
2
B: Hypothetical protein
D: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3734
Polymers51,9822
Non-polymers3902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint2 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.527, 68.522, 79.570
Angle α, β, γ (deg.)69.29, 75.14, 93.73
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEUSERAA2 - 12021 - 139
21LEUSERBB2 - 12021 - 139
31LEUSERCC2 - 12021 - 139
41LEUSERDD2 - 12021 - 139
52ASPILEAA140 - 201159 - 220
62ASPILEBB140 - 201159 - 220
72ASPILECC140 - 201159 - 220
82ASPILEDD140 - 201159 - 220

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Components

#1: Protein
Hypothetical protein /


Mass: 25991.047 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Gene: XP_626409 / Plasmid: P28A-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Rosetta-R3 / References: UniProt: Q5CTR0
#2: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 21% PEG3350, 0.3 M NaBr, 0.1 M MES pH 5.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97953, 0.97967
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 7, 2005
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979531
20.979671
ReflectionResolution: 2.3→50 Å / Num. all: 40584 / Num. obs: 40584 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 20.25
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 4.55 / Num. unique all: 3974 / Rsym value: 0.283 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVERESOLVEphasing
Omodel building
Cootmodel building
CCP4phasing
ARP/wARPmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.866 / SU B: 16.522 / SU ML: 0.217 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.459 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28024 2091 5.2 %RANDOM
Rwork0.21968 ---
all0.22279 38493 --
obs0.22279 38493 98.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.229 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å2-0.07 Å20.17 Å2
2---0.39 Å20.31 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6639 0 48 428 7115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0227053
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7541.9769584
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.5555857
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02724.481337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.164151257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5621543
X-RAY DIFFRACTIONr_chiral_restr0.150.21027
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025419
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2350.23309
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.24771
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.2428
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3340.266
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2750.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7021.54233
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.20326935
X-RAY DIFFRACTIONr_scbond_it1.93732820
X-RAY DIFFRACTIONr_scangle_it2.8454.52649
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1311 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.310.5
2Bmedium positional0.330.5
3Cmedium positional0.320.5
4Dmedium positional0.310.5
1Amedium thermal1.272
2Bmedium thermal0.912
3Cmedium thermal0.822
4Dmedium thermal0.762
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 158 -
Rwork0.239 2846 -
obs--97.63 %
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)
14.2367-0.85741.65143.1752-0.8445.37620.22230.2220.1409-0.1882-0.099-0.09060.15340.0503-0.1233-0.04710.0317-0.006-0.14620.001-0.061261.0693.943375.0098
21.9678-0.13780.40560.6472-0.30571.37380.01950.05440.00850.03930.0018-0.0046-0.1420.1044-0.0213-0.04090.0083-0.0105-0.14220.0004-0.038468.58583.757981.3356
32.5479-1.5410.35272.6375-0.60270.3208-0.1648-0.2369-0.07480.16560.11780.1909-0.2073-0.09320.047-0.02850.0284-0.0281-0.0668-0.0234-0.036855.750489.307280.1119
42.96860.03260.38450.6347-0.31351.73270.0019-0.00550.08430.10370.03980.01320.0319-0.1038-0.0418-0.0130.0184-0.0258-0.12270.011-0.075364.283375.031688.2662
52.62250.1791-0.05651.23660.1510.80640.11020.0269-0.16440.0956-0.02090.020.07650.0782-0.0893-0.0718-0.01850.0285-0.12350.0005-0.054156.538845.144277.7929
60.88230.0673-0.64080.7081-0.29382.0814-0.0264-0.1067-0.074-0.04320.0069-0.0690.10470.25430.0195-0.0899-0.0081-0.015-0.0819-0.0104-0.002567.278354.247471.0055
71.39570.20830.62851.5641-1.21081.3933-0.04860.20510.0189-0.05390.19590.18310.2382-0.0795-0.1472-0.0818-0.02660.0068-0.0537-0.0243-0.030150.479251.999973.1533
82.6483-0.47310.54732.8535-0.85012.2231-0.0061-0.06290.034-0.09410.03290.0234-0.0625-0.0866-0.0268-0.1055-0.01310.0464-0.0791-0.0077-0.080161.844864.095165.2045
90.8340.3357-0.08411.2954-1.38397.75920.0082-0.0158-0.1882-0.13380.0258-0.15060.4340.2524-0.0340.06870.1016-0.0064-0.05550.009-0.053576.528658.8295117.1626
100.70810.0447-0.4550.7424-0.70893.32210.0637-0.0267-0.09390.0444-0.0575-0.06390.15240.344-0.0062-0.04390.0298-0.0513-0.065-0.017-0.023776.898870.0959108.5768
111.78270.02640.59350.5087-0.86011.68290.1005-0.0004-0.0282-0.24390.08080.22570.49020.0246-0.18130.09820.0075-0.0601-0.0267-0.0039-0.033568.164161.2815114.8172
125.80760.6570.07561.1469-0.11243.21030.0623-0.16140.0958-0.0320.0540.0962-0.1119-0.0546-0.11630.00170.0245-0.0202-0.07180.0023-0.067367.932676.3033104.4268
130.7760.0589-0.00252.6216-2.65649.24560.0381-0.0272-0.040.015-0.0792-0.2825-0.18450.3590.0412-0.0592-0.03620.0579-0.04740.0223-0.036774.150279.82636.4129
140.8563-0.1393-0.06261.3601-0.81532.2390.01790.14740.0007-0.2212-0.0216-0.12690.12090.17120.0037-0.0567-0.03690.0416-0.0246-0.0167-0.024472.682668.084243.4811
151.08130.4442-0.42132.4117-1.86241.94240.1078-0.0547-0.03360.03190.21710.128-0.1796-0.2592-0.3249-0.0012-0.03820.0090.00640.0111-0.034465.298578.551238.5777
163.2377-0.1373-1.59082.7623-0.2264.2395-0.01480.0494-0.0276-0.22820.17240.01850.3464-0.1416-0.15760.0087-0.08040.0062-0.05790.0028-0.081463.032962.986548.1761
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 4319 - 62
2X-RAY DIFFRACTION2AA44 - 12563 - 144
3X-RAY DIFFRACTION3AA126 - 164145 - 183
4X-RAY DIFFRACTION4AA165 - 204184 - 223
5X-RAY DIFFRACTION5BB0 - 4319 - 62
6X-RAY DIFFRACTION6BB44 - 11763 - 136
7X-RAY DIFFRACTION7BB118 - 164137 - 183
8X-RAY DIFFRACTION8BB165 - 204184 - 223
9X-RAY DIFFRACTION9CC0 - 4319 - 62
10X-RAY DIFFRACTION10CC44 - 12563 - 144
11X-RAY DIFFRACTION11CC126 - 164145 - 183
12X-RAY DIFFRACTION12CC165 - 204184 - 223
13X-RAY DIFFRACTION13DD1 - 4220 - 61
14X-RAY DIFFRACTION14DD43 - 12562 - 144
15X-RAY DIFFRACTION15DD126 - 164145 - 183
16X-RAY DIFFRACTION16DD165 - 204184 - 223

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