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- PDB-3cu3: Crystal structure of a domain of unknown function with a cystatin... -

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Basic information

Entry
Database: PDB / ID: 3cu3
TitleCrystal structure of a domain of unknown function with a cystatin-like fold (npun_r1993) from nostoc punctiforme pcc 73102 at 2.00 A resolution
ComponentsDomain of unknown function with a cystatin-like fold
KeywordsMETAL BINDING PROTEIN / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Domain of unknown function DUF4440 / Domain of unknown function (DUF4440) / Steroid delta5-4-isomerase / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Domain of unknown function with a cystatin-like fold
Similarity search - Component
Biological speciesNostoc punctiforme (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Domain of Unknown Function with a Cystatin-like Fold (ZP_00107529.1) from Nostoc punctiforme PCC 73102 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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: Domain of unknown function with a cystatin-like fold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7377
Polymers19,3581
Non-polymers3796
Water2,612145
1
A: Domain of unknown function with a cystatin-like fold
hetero molecules

A: Domain of unknown function with a cystatin-like fold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,47414
Polymers38,7162
Non-polymers75712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y+1/2,z1
Buried area4400 Å2
ΔGint-34.4 kcal/mol
Surface area15160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.510, 71.900, 117.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein Domain of unknown function with a cystatin-like fold


Mass: 19358.166 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme (bacteria) / Strain: PCC 73102 / Gene: ZP_00107529.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: D0VWT9*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Sequence details1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED ...1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. 2. THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. THE SEQUENCE INFORMATION IS AVAILABLE AT GENBANK WITH ACCESSION CODE ZP_00107529.1

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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: 2.76 Å3/Da / Density % sol: 55.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.47
Details: NANODROP, 0.2M Magnesium chloride, 36.0% PEG 400, 0.1M HEPES pH 7.47, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837, 0.97905, 0.97929
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 17, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979051
30.979291
ReflectionResolution: 2→29.386 Å / Num. obs: 14803 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.61 % / Biso Wilson estimate: 17.709 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 7.97
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.070.382.2650342650197.8
2.07-2.150.295352002705199.4
2.15-2.250.2393.554892853199.3
2.25-2.370.203454392819198.7
2.37-2.520.1724.853842785199.3
2.52-2.710.1395.853142742199.2
2.71-2.990.1017.755082832199
2.99-3.420.06611.253102723198.6
3.42-4.30.03917.553762758198.7
4.3-29.3860.03419.854122763198.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.004data extraction
MAR345CCDdata collection
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2→29.386 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.161 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.142
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. MG ION AND POLYETHYLENE GLYCOL MOLECULE FROM CRYSTALLIZATION CONDITION HAVE BEEN MODELED IN THE STRUCTURE. ETHYLENE GLYCOL MOLECULES FROM CRYO SOLUTION ARE ALSO MODELED IN THIS STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.216 751 5.1 %RANDOM
Rwork0.161 ---
obs0.164 14802 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.479 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20 Å2
2--1.46 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 2→29.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1262 0 24 145 1431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221330
X-RAY DIFFRACTIONr_bond_other_d0.0010.02902
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.9451793
X-RAY DIFFRACTIONr_angle_other_deg1.04832180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9835167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72523.84665
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77315215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7521511
X-RAY DIFFRACTIONr_chiral_restr0.0920.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021501
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02288
X-RAY DIFFRACTIONr_mcbond_it2.0633819
X-RAY DIFFRACTIONr_mcbond_other0.6123337
X-RAY DIFFRACTIONr_mcangle_it3.24351320
X-RAY DIFFRACTIONr_scbond_it5.568511
X-RAY DIFFRACTIONr_scangle_it8.13211473
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 64 -
Rwork0.178 999 -
all-1063 -
obs--98.79 %

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