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- PDB-4mz1: Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase, ... -

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Basic information

Entry
Database: PDB / ID: 4mz1
TitleCrystal Structure of the Inosine 5'-monophosphate Dehydrogenase, with a Internal Deletion of CBS Domain from Campylobacter jejuni complexed with inhibitor compound P12
ComponentsInosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / TIM barrel / alpha-beta structure / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
IMP dehydrogenase / GMP reductase domain / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain ...IMP dehydrogenase / GMP reductase domain / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / 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
Chem-2F1 / ACETIC ACID / INOSINIC ACID / : / PHOSPHATE ION / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3991 Å
AuthorsKim, Y. / Makowska-Grzyska, M. / Gu, M. / Anderson, W.F. / Joachimiak, A. / CSGID / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published / Year: 2013
Title: Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase, with a Internal Deletion of CBS Domain from Campylobacter jejuni complexed with inhibitor compound P12
Authors: Kim, Y. / Makowska-Grzyska, M. / Gu, M. / Anderson, W.F. / Joachimiak, A.
History
DepositionSep 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase
C: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,51524
Polymers123,1603
Non-polymers3,35621
Water3,639202
1
A: Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,77932
Polymers164,2134
Non-polymers4,56628
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 area24600 Å2
ΔGint-199 kcal/mol
Surface area49250 Å2
MethodPISA
2
B: Inosine-5'-monophosphate dehydrogenase
hetero molecules

B: Inosine-5'-monophosphate dehydrogenase
hetero molecules

B: Inosine-5'-monophosphate dehydrogenase
hetero molecules

B: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,78332
Polymers164,2134
Non-polymers4,57128
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area25610 Å2
ΔGint-224 kcal/mol
Surface area49580 Å2
MethodPISA
3
C: Inosine-5'-monophosphate dehydrogenase
hetero molecules

C: Inosine-5'-monophosphate dehydrogenase
hetero molecules

C: Inosine-5'-monophosphate dehydrogenase
hetero molecules

C: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,50032
Polymers164,2134
Non-polymers4,28728
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area24230 Å2
ΔGint-183 kcal/mol
Surface area51590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.062, 118.062, 435.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-506-

PO4

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / IMPD / IMPDH


Mass: 41053.176 Da / Num. of mol.: 3 / Fragment: IMPDH-delta-S-CBS / Mutation: CBS domain (residues 92-195) is replaced with G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter)
Strain: NCTC 11168 / Gene: guaB, Cj1058c / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q0P9J4, IMP dehydrogenase

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Non-polymers , 7 types, 223 molecules

#2: Chemical ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical ChemComp-2F1 / 1-(4-bromophenyl)-3-{2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}urea


Mass: 373.287 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H21BrN2O
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 3.08 Å3/Da / Density % sol: 60.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 0.2 M lithium sulfate, 0.1 M CAPS pH 10.5, 1.2 M NaH(2)PO4/0.8 M K(2)HPO4, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2012 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.399→50 Å / Num. all: 58784 / Num. obs: 58784 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 33.98 Å2 / Rsym value: 0.146 / Net I/σ(I): 7.3
Reflection shellResolution: 2.399→2.44 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 2723 / Rsym value: 0.706 / % possible all: 91.3

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: dev_1367)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4MYA

4mya


Resolution: 2.3991→45.574 Å / SU ML: 0.26 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2968 5.05 %random
Rwork0.172 ---
all0.174 58736 --
obs0.174 58736 96.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.6 Å2
Refinement stepCycle: LAST / Resolution: 2.3991→45.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7945 0 199 202 8346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088331
X-RAY DIFFRACTIONf_angle_d1.1511258
X-RAY DIFFRACTIONf_dihedral_angle_d14.2163086
X-RAY DIFFRACTIONf_chiral_restr0.0671298
X-RAY DIFFRACTIONf_plane_restr0.0051430
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.3991-2.43840.28671220.24962480260291
2.4384-2.48050.23891220.21892566268895
2.4805-2.52560.27521460.20312636278297
2.5256-2.57410.30441450.21062639278498
2.5741-2.62670.24881250.20092669279498
2.6267-2.68380.27051510.19312663281498
2.6838-2.74620.26591640.20662628279298
2.7462-2.81490.24171210.20722697281898
2.8149-2.8910.30871370.20582665280298
2.891-2.9760.24351540.20162644279898
2.976-3.0720.24261300.20742687281798
3.072-3.18180.25741450.19692683282898
3.1818-3.30920.22491580.18792635279398
3.3092-3.45970.24571620.17882665282798
3.4597-3.64210.21221440.16042656280097
3.6421-3.87010.16961630.15412651281497
3.8701-4.16880.17731330.12792679281297
4.1688-4.58790.16571450.12342680282597
4.5879-5.2510.15461330.12452678281195
5.251-6.61250.18711320.1692716284895
6.6125-45.58250.16971360.17162751288791
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)
11.8344-0.21430.01160.735-0.09841.6008-0.002-0.0711-0.03580.06180.01090.13240.0924-0.0812-0.0060.226-0.01810.03150.18030.0420.19136.498242.88627.2249
21.9319-0.6103-0.15792.53410.11851.77630.07140.4028-0.28760.1973-0.24210.58270.3208-0.50460.13190.2668-0.07850.01390.4138-0.01090.407117.642545.046219.1224
30.3965-0.2223-0.09980.36730.3020.23730.009-0.02790.03510.11750.04330.1018-0.0084-0.1111-0.0390.2364-0.01520.04380.25990.03920.254630.538853.454930.8742
40.5313-0.1495-0.81861.7314-0.18962.07830.00170.13710.2025-0.30360.1097-0.0646-0.1174-0.1398-0.0340.31990.01010.01950.2539-0.01010.192936.596649.70753.7341
50.49920.3125-0.0440.83480.13161.24960.04360.09560.0451-0.2523-0.0688-0.1292-0.00090.04520.00140.1819-0.02830.01680.2027-0.01540.189336.929548.207415.9137
61.33250.2112-0.75251.01340.06641.06480.00080.03660.12470.02660.10420.0560.0695-0.0167-0.02040.23830.0196-0.03250.28990.05610.25651.048341.706924.9364
71.8926-0.0657-0.33120.66540.37651.1890.0347-0.09860.13140.09250.0241-0.098-0.05060.0461-0.06560.27440.0022-0.02310.2235-0.00950.242318.745119.943495.6913
81.5202-0.3135-0.00672.17240.36261.4793-0.0910.13960.07850.01140.1262-0.3799-0.27710.2573-0.01360.2483-0.07260.0110.2854-0.03680.214637.995321.765488.1654
90.5038-0.40130.21220.5924-0.10260.5848-0.0307-0.09050.09870.06740.0312-0.07260.0196-0.0446-0.03360.2254-0.0186-0.01510.2017-0.03740.211726.729911.04699.6751
100.9018-0.0852-0.02130.79440.11091.03510.01990.1205-0.022-0.0412-0.04720.08490.08040.13930.02190.23540.0146-0.00090.2267-0.00230.18619.893614.044580.4241
111.06170.37130.55411.05680.05930.92760.0211-0.09530.0455-0.02290.00350.1222-0.05270.02920.02240.2227-0.0130.01030.2296-0.01790.2434.430318.592493.5581
120.6605-0.4369-0.19391.37150.06311.22910.03790.06030.1092-0.1228-0.04880.0191-0.0927-0.10330.0130.20350.02090.04070.2540.03050.269812.412625.096441.5837
132.8478-0.37390.03830.9374-0.07381.23860.0633-0.35240.31750.1696-0.00240.0333-0.3232-0.1408-0.04660.2881-0.00260.10950.2336-0.01460.39463.715441.82753.0568
141.02270.3293-0.25821.6598-0.18341.15150.01940.09620.2067-0.00950.0316-0.0343-0.03740.0592-0.03940.2422-0.0030.02810.26010.04340.30674.052633.351740.5887
151.41140.51240.74041.04660.12271.36210.0039-0.25990.03270.06330.07250.0736-0.1726-0.1462-0.02840.25370.02750.02760.3044-0.00060.18890.093624.416561.1444
161.05780.0303-0.0381.10150.25291.26280.08530.26720.1165-0.17870.0708-0.1808-0.08470.1223-0.08490.16880.01760.03310.23950.01770.213117.799216.846740.2397
172.62990.2170.77860.44-0.95882.73320.0305-0.17480.08970.2329-0.11190.30850.1961-0.2603-0.14440.3179-0.01250.04670.2751-0.0160.342716.03977.034756.5096
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 62 )
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 236 )
3X-RAY DIFFRACTION3chain 'A' and (resid 237 through 361 )
4X-RAY DIFFRACTION4chain 'A' and (resid 362 through 382 )
5X-RAY DIFFRACTION5chain 'A' and (resid 383 through 441 )
6X-RAY DIFFRACTION6chain 'A' and (resid 442 through 482 )
7X-RAY DIFFRACTION7chain 'B' and (resid 0 through 63 )
8X-RAY DIFFRACTION8chain 'B' and (resid 64 through 236 )
9X-RAY DIFFRACTION9chain 'B' and (resid 237 through 361 )
10X-RAY DIFFRACTION10chain 'B' and (resid 362 through 441 )
11X-RAY DIFFRACTION11chain 'B' and (resid 442 through 482 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 62 )
13X-RAY DIFFRACTION13chain 'C' and (resid 63 through 86 )
14X-RAY DIFFRACTION14chain 'C' and (resid 87 through 361 )
15X-RAY DIFFRACTION15chain 'C' and (resid 362 through 422 )
16X-RAY DIFFRACTION16chain 'C' and (resid 423 through 466 )
17X-RAY DIFFRACTION17chain 'C' and (resid 467 through 482 )

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