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- PDB-1vrd: Crystal structure of Inosine-5'-monophosphate dehydrogenase (TM13... -

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Basic information

Entry
Database: PDB / ID: 1vrd
TitleCrystal structure of Inosine-5'-monophosphate dehydrogenase (TM1347) from THERMOTOGA MARITIMA at 2.18 A resolution
Componentsinosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE / TM1347 / Inosine-5'-monophosphate dehydrogenase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


IMP dehydrogenase / IMP dehydrogenase activity / GMP biosynthetic process / GTP biosynthetic process / nucleotide binding / metal ion binding
Similarity search - Function
IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain ...IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Inosine-5'-monophosphate dehydrogenase (TM1347) from THERMOTOGA MARITIMA at 2.18 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: inosine-5'-monophosphate dehydrogenase
B: inosine-5'-monophosphate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)107,0942
Polymers107,0942
Non-polymers00
Water3,711206
1
A: inosine-5'-monophosphate dehydrogenase

A: inosine-5'-monophosphate dehydrogenase

A: inosine-5'-monophosphate dehydrogenase

A: inosine-5'-monophosphate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)214,1874
Polymers214,1874
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area9070 Å2
ΔGint-64 kcal/mol
Surface area49800 Å2
MethodPISA, PQS
2
B: inosine-5'-monophosphate dehydrogenase

B: inosine-5'-monophosphate dehydrogenase

B: inosine-5'-monophosphate dehydrogenase

B: inosine-5'-monophosphate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)214,1874
Polymers214,1874
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area8860 Å2
ΔGint-66 kcal/mol
Surface area48110 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)120.083, 120.083, 144.079
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B
171A
181B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETTHRTHR3AA1 - 8513 - 97
21METMETLYSLYS3BB1 - 8313 - 95
32ILEILEHISHIS6AA197 - 203209 - 215
42SERSERHISHIS6BB199 - 203211 - 215
53PROPROSERSER3AA204 - 299216 - 311
63PROPROSERSER3BB204 - 299216 - 311
74ILEILETHRTHR6AA300 - 303312 - 315
84ILEILETHRTHR6BB300 - 303312 - 315
95ARGARGGLUGLU3AA304 - 369316 - 381
105ARGARGGLUGLU3BB304 - 369316 - 381
116THRTHRLEULEU6AA370 - 372382 - 384
126THRTHRLEULEU6BB370 - 372382 - 384
137TYRTYRLYSLYS3AA373 - 379385 - 391
147TYRTYRLYSLYS3BB373 - 379385 - 391
158ALAALAVALVAL6AA380 - 415392 - 427
168ALAALAVALVAL6BB380 - 415392 - 427
179PROPROTHRTHR3AA416 - 457428 - 469
189PROPROTHRTHR3BB416 - 457428 - 469

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Components

#1: Protein inosine-5'-monophosphate dehydrogenase


Mass: 53546.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM1347 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X168, IMP dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 3.8 Å3/Da / Density % sol: 67.42 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4
Details: 40% MPD, 0.1M citric acid pH 4.0, final pH 4, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1
DetectorType: ADSC / Detector: CCD / Date: Oct 21, 2001
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→46.12 Å / Num. obs: 50043 / % possible obs: 94.49 % / Redundancy: 4.11 % / Biso Wilson estimate: 44.79 Å2 / Rsym value: 0.078 / Net I/σ(I): 14.26
Reflection shellResolution: 2.18→2.2 Å / Redundancy: 3.26 % / Mean I/σ(I) obs: 1.51 / Num. unique all: 1308 / Rsym value: 0.574 / % possible all: 75.52

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1zfj

1zfj


Resolution: 2.18→46.12 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.918 / SU B: 9.083 / SU ML: 0.135 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. THE FOLLOWING REGIONS ARE DISORDERED: A86-196, A385-409, A458-482, B84-198, B385-409, B458-482. FRAGMENTS OF DENSITY IS PRESENT, NO MODEL WAS BUILT FOR THESE AREAS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25759 2553 5.1 %RANDOM
Rwork0.21653 ---
obs0.21863 47472 94.22 %-
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: 39.358 Å2
Baniso -1Baniso -2Baniso -3
1--2.2 Å20 Å20 Å2
2---2.2 Å20 Å2
3---4.41 Å2
Refinement stepCycle: LAST / Resolution: 2.18→46.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4670 0 0 206 4876
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224725
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.9856397
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9355632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.07123.851161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.27615822
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7251533
X-RAY DIFFRACTIONr_chiral_restr0.0920.2779
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023423
X-RAY DIFFRACTIONr_nbd_refined0.2130.22300
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2291
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.290
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.212
X-RAY DIFFRACTIONr_mcbond_it2.07333242
X-RAY DIFFRACTIONr_mcangle_it3.08355053
X-RAY DIFFRACTIONr_scbond_it6.05781646
X-RAY DIFFRACTIONr_scangle_it8.37111344
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23294
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1176tight positional0.050.05
1119loose positional0.425
1176tight thermal0.20.5
1119loose thermal2.9810
LS refinement shellResolution: 2.18→2.237 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 172 5.89 %
Rwork0.234 2747 -
obs--75.29 %
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)
11.7006-0.17910.12491.6796-0.00340.46490.02540.14730.0013-0.1068-0.0009-0.0775-0.05220.0773-0.0245-0.0542-0.02540.0048-0.0418-0.023-0.14285.619878.17023.3142
22.14620.10450.05531.1813-0.13190.90580.0624-0.17530.33560.05850.00910.0237-0.2569-0.0382-0.07160.0596-0.00350.0761-0.0518-0.0282-0.078460.258891.1584-46.7066
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 9 - 436 / Label seq-ID: 21 - 448

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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