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- PDB-3ryd: Crystal structure of Ca bound IMPase family protein from Staphylo... -

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Basic information

Entry
Database: PDB / ID: 3ryd
TitleCrystal structure of Ca bound IMPase family protein from Staphylococcus aureus
ComponentsInositol monophosphatase family protein
KeywordsHYDROLASE / IMPase fold / FIG superfamily protein / phosphatase
Function / homology
Function and homology information


D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / S,R MESO-TARTARIC ACID / :
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.37 Å
AuthorsBhattacharyya, S. / Dutta, D. / Ghosh, A.K. / Das, A.K.
CitationJournal: Biochimie / Year: 2012
Title: Crystal structure of Staphylococcal dual specific inositol monophosphatase/NADP(H) phosphatase (SAS2203) delineates the molecular basis of substrate specificity
Authors: Bhattacharyya, S. / Dutta, D. / Saha, B. / Ghosh, A.K. / Das, A.K.
History
DepositionMay 11, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Sep 16, 2020Group: Database references / Derived calculations / Structure summary
Category: pdbx_struct_conn_angle / struct ...pdbx_struct_conn_angle / struct / struct_conn / struct_ref_seq_dif / struct_site
Item: _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct.title / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inositol monophosphatase family protein
C: Inositol monophosphatase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,60411
Polymers62,9162
Non-polymers6889
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.878, 68.046, 143.898
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 Inositol monophosphatase family protein / IMPase family protein


Mass: 31458.146 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MSSA476 / Gene: SAS2203 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q6G709, inositol-phosphate phosphatase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 1.98 Å3/Da / Density % sol: 37.86 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.15M Sodium Potassium tartrate, 22%(w/v) PEG 3350, 0.1M HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 7, 2011 / Details: mirrors
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.367→71.949 Å / Num. all: 20973 / Num. obs: 20973 / % possible obs: 99.2 % / Redundancy: 7 % / Rsym value: 0.132 / Net I/σ(I): 13.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.37-2.496.70.6740.6211.21940329110.2570.6740.6213.595.9
2.49-2.657.10.4990.4621.52025028490.1860.4990.4625100
2.65-2.837.10.3620.33621960127430.1350.3620.3366.7100
2.83-3.067.20.2650.2462.81785224920.0990.2650.2468.9100
3.06-3.357.20.1720.1594.21675323320.0640.1720.15913.3100
3.35-3.747.10.1290.1195.71522921330.0480.1290.11918.8100
3.74-4.327.10.0740.0699.91343218830.0280.0740.06925.4100
4.32-5.297.10.0540.0513.21153416280.020.0540.0529.4100
5.29-7.486.90.0650.0611889012830.0240.0650.0623.9100
7.48-19.8666.40.0430.041446077190.0170.0430.0433.594.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→19.68 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.872 / WRfactor Rfree: 0.2513 / WRfactor Rwork: 0.1713 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.815 / SU B: 20.591 / SU ML: 0.225 / SU R Cruickshank DPI: 0.5914 / SU Rfree: 0.3134 / Cross valid method: THROUGHOUT / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2784 1070 5.1 %RANDOM
Rwork0.1899 ---
obs0.1945 20921 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 58.01 Å2 / Biso mean: 28.8 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å20 Å20 Å2
2---2.37 Å20 Å2
3---1.03 Å2
Refinement stepCycle: LAST / Resolution: 2.37→19.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4098 0 36 180 4314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224210
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.9645690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3495508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.24725.787197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.52315749
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.783159
X-RAY DIFFRACTIONr_chiral_restr0.1150.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213156
X-RAY DIFFRACTIONr_mcbond_it0.6741.52557
X-RAY DIFFRACTIONr_mcangle_it1.24524113
X-RAY DIFFRACTIONr_scbond_it2.09631653
X-RAY DIFFRACTIONr_scangle_it3.2464.51577
LS refinement shellResolution: 2.367→2.428 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 82 -
Rwork0.237 1349 -
all-1431 -
obs--92.56 %
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)
11.0502-0.2246-0.22661.91830.34621.47340.0304-0.00020.001-0.2233-0.03910.1598-0.0332-0.06510.00870.0322-0.0077-0.0280.02790.01470.0285-7.956711.3029-36.6083
21.45970.0934-0.27092.8911-0.91951.3834-0.0175-0.1662-0.190.4161-0.00260.1857-0.06270.00270.02020.0869-0.00840.03450.05450.02170.0404-5.81143.1095-6.5736
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 265
2X-RAY DIFFRACTION2C3 - 265

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