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- PDB-1vko: Crystal structure of inositol-3-phosphate synthase (ce21227) from... -

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Basic information

Entry
Database: PDB / ID: 1vko
TitleCrystal structure of inositol-3-phosphate synthase (ce21227) from Caenorhabditis elegans at 2.30 A resolution
Componentsinositol-3-phosphate synthase
KeywordsISOMERASE / ce21227 / INOSITOL-3-PHOSPHATE SYNTHASE / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics
Function / homology
Function and homology information


Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PYROPHOSPHATE 2- / :
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of inositol-3-phosphate synthase (ce21227) from Caenorhabditis elegans at 2.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 25, 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_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.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_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_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
Revision 1.5Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: inositol-3-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2108
Polymers60,0071
Non-polymers1,2037
Water2,684149
1
A: inositol-3-phosphate synthase
hetero molecules

A: inositol-3-phosphate synthase
hetero molecules

A: inositol-3-phosphate synthase
hetero molecules

A: inositol-3-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,84032
Polymers240,0274
Non-polymers4,81328
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area39550 Å2
ΔGint-330 kcal/mol
Surface area65240 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)76.980, 129.980, 131.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 1 molecules A

#1: Protein inositol-3-phosphate synthase


Mass: 60006.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: ce21227 / Production host: Escherichia coli (E. coli) / References: UniProt: Q18664, inositol-3-phosphate synthase

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Non-polymers , 6 types, 156 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#6: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.7455.04
22.7855.43
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop
Details: 0.12M Na Cl, 0.90M Tartrate_K Na, 0.084M Imidazole, 0.016M Imidazole Chloride , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.977757
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 27, 2002 / Details: FLAT MIRROR
RadiationMonochromator: SINGLE CRYSTAL SI(311) BENT MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977757 Å / Relative weight: 1
ReflectionResolution: 2.3→29.41 Å / Num. obs: 28995 / % possible obs: 98 % / Redundancy: 3.9 % / Biso Wilson estimate: 49.54 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 14.5
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 3.9 / Num. unique all: 4221 / % possible all: 98.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
SHELXDphasing
autoSHARPphasing
REFMAC5.2.0003refinement
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Obtained from MAD data of a crystal of SE-MET substituted protein in space group P21 21 2

Resolution: 2.3→29.41 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.915 / SU B: 16.544 / SU ML: 0.2 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.297 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: EXTRA DENSITY IN THE ACTIVE SITE WAS TENTATIVELY MODELED AS PYROPHOSPHATE BASED ON THE FIT TO ELECTRON DENSITY. ONE POTASSIUM, TWO CHLORINES AND TWO IODIDES ARE MODELED. THESE ENTITIES ARE ...Details: EXTRA DENSITY IN THE ACTIVE SITE WAS TENTATIVELY MODELED AS PYROPHOSPHATE BASED ON THE FIT TO ELECTRON DENSITY. ONE POTASSIUM, TWO CHLORINES AND TWO IODIDES ARE MODELED. THESE ENTITIES ARE POTENTIALLY FROM THE CRYSTALLIZATION BUFFERS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26455 1470 5.1 %RANDOM
Rwork0.20035 ---
obs0.20352 27525 97.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.35 Å2
Baniso -1Baniso -2Baniso -3
1-4.39 Å20 Å20 Å2
2--1.05 Å20 Å2
3----5.43 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4007 0 58 149 4214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224159
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.9615657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9445510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.46824.731186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.57715694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6421518
X-RAY DIFFRACTIONr_chiral_restr0.1110.2635
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023138
X-RAY DIFFRACTIONr_nbd_refined0.2310.21882
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2218
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.2158
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.221
X-RAY DIFFRACTIONr_mcbond_it1.97632557
X-RAY DIFFRACTIONr_mcangle_it3.43354159
X-RAY DIFFRACTIONr_scbond_it6.73281620
X-RAY DIFFRACTIONr_scangle_it8.73111498
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22789
X-RAY DIFFRACTIONr_metal_ion_refined0.1520.23
LS refinement shellResolution: 2.299→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 108 5.18 %
Rwork0.275 1976 -
obs--96.44 %
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)
10.16550.1861-0.18510.2367-0.05811.0279-0.0047-0.02020.1208-0.04360.05690.00260.34620.202-0.0522-0.04330.1051-0.0115-0.0449-0.02090.002212.681542.281650.6398
23.5835-1.261-3.09333.9456-0.06523.05020.1966-0.17190.0739-0.0983-0.01280.18270.30940.1057-0.18380.0977-0.0156-0.0943-0.09280.0168-0.13410.666823.251275.9671
35.7373-2.17060.99750.8212-0.37740.17340.36360.22830.27540.2017-0.4305-0.1231-0.1313-0.02060.0669-0.00840.06770.06670.0055-0.028-0.018817.758153.555344.7565
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A

IDRefine TLS-IDLabel asym-IDAuth seq-IDLabel seq-ID
11A11 - 50123 - 513
22A502 - 521514 - 533
33G6011

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