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- PDB-3b5p: Crystal structure of a cadd-like protein of unknown function (npu... -

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Basic information

Entry
Database: PDB / ID: 3b5p
TitleCrystal structure of a cadd-like protein of unknown function (npun_f6505) from nostoc punctiforme pcc 73102 at 2.00 A resolution
ComponentsCADD-like protein of unknown function
KeywordsOXIDOREDUCTASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyProtein of unknown function DUF3865, CADD-like / Domain of Unknown Function with PDB structure (DUF3865) / Heme oxygenase-like / Heme Oxygenase; Chain A / Haem oxygenase-like, multi-helical / Up-down Bundle / Mainly Alpha / CADD-like protein of unknown function
Function and homology information
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 CADD-like protein of unknown function (ZP_00108531.1) from Nostoc punctiforme PCC 73102 at 2.00 A resolution (monoclinic form)
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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
Remark 999 SEQUENCE 1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE 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_00108531.1 AND FROM THE UNIPROT ARCHIVE (UNIPARC) UNDER ACCESSION ID UPI000038D4FF.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CADD-like protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6924
Polymers27,5061
Non-polymers1863
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.670, 78.510, 45.580
Angle α, β, γ (deg.)90.000, 112.290, 90.000
Int Tables number4
Space group name H-MP1211
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein CADD-like protein of unknown function


Mass: 27505.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme (bacteria) / Strain: PCC 73102 / Gene: ZP_00108531.1 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: D0VWS1*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsREMARK 999 REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG ...REMARK 999 REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.33 Å3/Da / Density % sol: 47.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: NANODROP, 0.2M Mg(OAc)2, 20.0% PEG 8000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0000, 0.9797, 0.9796
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 14, 2007
RadiationMonochromator: Double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97971
30.97961
ReflectionResolution: 2→28.736 Å / Num. obs: 16846 / % possible obs: 91.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 27.36 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 6.85
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.060.4311.523612237166
2.06-2.140.358237853137193.7
2.14-2.240.2612.640343318194.6
2.24-2.360.2063.339273274194.3
2.36-2.510.1714.139933327194.7
2.51-2.70.1335.138503163194.8
2.7-2.970.0916.939003269195
2.97-3.40.0659.738773247194.9
3.4-4.270.04214.337763267195.3
4.27-28.7360.02917.138473318194.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→28.736 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.931 / SU B: 8.38 / SU ML: 0.118 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.163
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. RAMACHANDRAN OUTLIER OF RESIDUE ASP 180 IN SUBUNIT A IS LOCATED IN POOR DENSITY. 5. RESIDUE GLU 183 IN SUBUNIT A IS DISORDERED AND NOT INCLUDED IN THE MODEL. 6. ETHYLENE GLYCOL (EDO) MOLECULES FROM CRYO SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.225 851 5.1 %RANDOM
Rwork0.167 ---
obs0.169 16827 98.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.038 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20 Å21.95 Å2
2---1.19 Å20 Å2
3---1.09 Å2
Refinement stepCycle: LAST / Resolution: 2→28.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1783 0 12 143 1938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221901
X-RAY DIFFRACTIONr_bond_other_d0.0010.021241
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9492584
X-RAY DIFFRACTIONr_angle_other_deg1.03133043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1435244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.60825.05985
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66615317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.276157
X-RAY DIFFRACTIONr_chiral_restr0.0850.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022160
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02383
X-RAY DIFFRACTIONr_nbd_refined0.2060.2414
X-RAY DIFFRACTIONr_nbd_other0.1690.21161
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2930
X-RAY DIFFRACTIONr_nbtor_other0.0850.2888
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.289
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1050.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2150.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.213
X-RAY DIFFRACTIONr_mcbond_it2.3431233
X-RAY DIFFRACTIONr_mcbond_other0.5843485
X-RAY DIFFRACTIONr_mcangle_it3.37451907
X-RAY DIFFRACTIONr_scbond_it5.9728785
X-RAY DIFFRACTIONr_scangle_it7.62811677
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 58 -
Rwork0.232 1076 -
all-1134 -
obs--89.43 %
Refinement TLS params.Method: refined / Origin x: -0.5189 Å / Origin y: 6.7533 Å / Origin z: 22.7767 Å
111213212223313233
T-0.0506 Å20.0053 Å2-0.0056 Å2--0.0248 Å2-0.0074 Å2---0.027 Å2
L0.3414 °2-0.2833 °20.0476 °2-1.2615 °2-0.5117 °2--0.6546 °2
S-0.0098 Å °-0.0128 Å °0.0151 Å °-0.0017 Å °-0.0466 Å °-0.1042 Å °0.0049 Å °0.0859 Å °0.0564 Å °

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