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- PDB-2opk: CRYSTAL STRUCTURE OF A PUTATIVE MANNOSE-6-PHOSPHATE ISOMERASE (RE... -

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Basic information

Entry
Database: PDB / ID: 2opk
TitleCRYSTAL STRUCTURE OF A PUTATIVE MANNOSE-6-PHOSPHATE ISOMERASE (REUT_A1446) FROM RALSTONIA EUTROPHA JMP134 AT 2.10 A RESOLUTION
ComponentsHypothetical protein
KeywordsISOMERASE / PUTATIVE MANNOSE-6-PHOSPHATE ISOMERASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Unknown ligand / Cupin type-2 domain-containing protein
Similarity search - Component
Biological speciesRalstonia eutropha (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (YP_295660.1) from Ralstonia eutropha JMP134 at 2.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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
Revision 1.6Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 300 BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE 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.

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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)50,13414
Polymers49,6384
Non-polymers49610
Water8,323462
1
A: Hypothetical protein
B: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0957
Polymers24,8192
Non-polymers2765
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-26 kcal/mol
Surface area10150 Å2
MethodPISA
2
C: Hypothetical protein
D: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0397
Polymers24,8192
Non-polymers2205
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-34 kcal/mol
Surface area10070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.580, 75.580, 198.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 4

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1MSEMSEAA1 - 1102 - 111
2MSEMSEBB1 - 1102 - 111
3PROPROCC3 - 1104 - 111
4MSEMSEDD1 - 1102 - 111
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
Hypothetical protein


Mass: 12409.479 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha (bacteria) / Species: Cupriavidus necator / Strain: JMP134 / Gene: YP_295660.1, Reut_A1446 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q471W7
#2: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 4 / Source method: obtained synthetically
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / 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: 2.86 Å3/Da / Density % sol: 56.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: NANODROP, 1.5M (NH4)2SO4, 12.0% Glycerol, 0.1M TRIS-HCL, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97876, 0.97904
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 7, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.978761
30.979041
ReflectionResolution: 2.1→28.41 Å / Num. obs: 34611 / % possible obs: 99.8 % / Biso Wilson estimate: 23.15 Å2 / Rmerge(I) obs: 0.135 / Net I/σ(I): 8.69
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
2.1-2.170.5342.5420733536898.3
2.17-2.260.423.423739612492
2.26-2.360.3833.722642582092.3
2.36-2.490.3474.124356626493.1
2.49-2.640.2884.922764584194.1
2.64-2.850.226.324664633395.7
2.85-3.130.1548.924030616597.3
3.13-3.590.09713.725059644198.2
3.590.05819.824744633199.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SOLVEphasing
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.1→28.41 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.967 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.153
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS 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 RECORD CONTAINS 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. ONE CHLORIDE ION AND FIVE GLYCEROL MOLECULES FROM CRYSTALLIZATION WERE MODELED INTO THE STRUCTURE. 5. ELECTRON DENSITY WAS OBSERVED NEAR THE PUTATIVE ACTIVE SITE RESIDUE 103 ON EACH SUBUNIT. THESE DENSITIES WERE MODELED AS AN UNKNOWN LIGAND (UNL). 6. UNINTERPRETABLE ELECTRON DENSITY IS OBSERVED BETWEEN THE SIDECHAINS OF GLU 54 AND TYR 48 OF THE C-SUBUNIT. THIS DENSITY WAS NOT MODELED. 7. RESIDUE 111 IN SUBUNIT A, RESIDUES 1 TO 2 AND 111 IN SUBUNIT C ARE DISORDERED AND NOT BUILT IN THIS MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1740 5 %RANDOM
Rwork0.166 ---
all0.168 ---
obs0.168 34529 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.641 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0.2 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3372 0 51 462 3885
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213572
X-RAY DIFFRACTIONr_bond_other_d0.0020.023133
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.944886
X-RAY DIFFRACTIONr_angle_other_deg1.00137276
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9985448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.49223.497163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.81215487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9981525
X-RAY DIFFRACTIONr_chiral_restr0.1380.2498
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024054
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02735
X-RAY DIFFRACTIONr_nbd_refined0.1850.3499
X-RAY DIFFRACTIONr_nbd_other0.1820.33088
X-RAY DIFFRACTIONr_nbtor_refined0.1760.51607
X-RAY DIFFRACTIONr_nbtor_other0.0880.52085
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.5526
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1670.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0710.33
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1670.329
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2710.523
X-RAY DIFFRACTIONr_mcbond_it2.02232301
X-RAY DIFFRACTIONr_mcbond_other0.7013895
X-RAY DIFFRACTIONr_mcangle_it2.89253576
X-RAY DIFFRACTIONr_scbond_it4.32881523
X-RAY DIFFRACTIONr_scangle_it5.916111305
Refine LS restraints NCS

Ens-ID: 1 / Number: 1514 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.40.5
2BMEDIUM POSITIONAL0.470.5
3CMEDIUM POSITIONAL0.460.5
4DMEDIUM POSITIONAL0.410.5
1AMEDIUM THERMAL12
2BMEDIUM THERMAL1.042
3CMEDIUM THERMAL1.262
4DMEDIUM THERMAL1.072
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 118 -
Rwork0.195 2351 -
obs-2469 99.16 %

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