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- PDB-2bwg: Structure of human guanosine monophosphate reductase GMPR1 in com... -

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Basic information

Entry
Database: PDB / ID: 2bwg
TitleStructure of human guanosine monophosphate reductase GMPR1 in complex with GMP
ComponentsGMP REDUCTASE I
KeywordsOXIDOREDUCTASE / NUCLEOTIDE PATHWAY / TIM BARREL
Function / homology
Function and homology information


GMP reductase complex / GMP reductase / Regulation of MITF-M dependent genes involved in invasion / GMP reductase activity / purine nucleotide metabolic process / Purine salvage / purine nucleobase metabolic process / response to cold / metal ion binding / cytosol
Similarity search - Function
GMP reductase / : / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase domain / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...GMP reductase / : / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase domain / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / : / GMP reductase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBunkoczi, G. / Haroniti, A. / Ng, S. / von Delft, F. / Gileadi, O. / Oppermann, U. / Arrowsmith, C. / Edwards, A. / Sundstrom, M.
CitationJournal: To be Published
Title: Structure of Human Guanosine Monophosphate Reductase Gmpr1 in Complex with Gmp
Authors: Bunkoczi, G. / Haroniti, A. / Ng, S. / von Delft, F. / Gileadi, O. / Oppermann, U. / Arrowsmith, C. / Edwards, A. / Sundstrom, M.
History
DepositionJul 13, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Oct 23, 2019Group: Data collection / Database references / Other / Category: pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_ref_seq_dif.details
Revision 1.5Dec 13, 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
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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC BB" IN EACH CHAIN ON SHEET RECORDS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC BB" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 9-STRANDED BARRELS REPRESENTED BY 10-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB DA" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 8-STRANDED BARRELS REPRESENTED BY 9-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GMP REDUCTASE I
B: GMP REDUCTASE I
C: GMP REDUCTASE I
D: GMP REDUCTASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,57512
Polymers159,9664
Non-polymers1,6098
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15200 Å2
ΔGint-88.7 kcal/mol
Surface area43480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.312, 114.418, 115.129
Angle α, β, γ (deg.)90.00, 102.74, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A2 - 339
2112B2 - 339
3112C2 - 339
4112D2 - 339

NCS oper:
IDCodeMatrixVector
1given(0.9208, 0.21745, -0.3238), (-0.3346, 0.01381, -0.94226), (-0.20042, 0.97597, 0.08547)-27.14677, -78.05757, -75.52034
2given(0.90924, -0.36989, -0.19094), (0.2045, -0.0026, 0.97886), (-0.36257, -0.92907, 0.07328)-16.18703, 80.67178, -76.3146
3given(0.82014, -0.13373, -0.55632), (-0.13359, -0.99018, 0.04108), (-0.55635, 0.04063, -0.82995)-46.05553, 2.96094, -151.1356

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Components

#1: Protein
GMP REDUCTASE I / GUANOSINE 5'-MONOPHOSPHATE OXIDOREDUCTASE 1 / GUANOSINE MONOPHOSPHATE REDUCTASE 1


Mass: 39991.539 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P36959, GMP reductase
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 1-22 CONSTITUTE A HIS-TAG THE SEQUENCE VARIANT AT RESIDUE 256 IS DESCRIBED BY THE UNIPROT ...RESIDUES 1-22 CONSTITUTE A HIS-TAG THE SEQUENCE VARIANT AT RESIDUE 256 IS DESCRIBED BY THE UNIPROT ENTRY P36959 AND GIVEN A VARIANT FEATURE TABLE ID VAR_003970

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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: 2.2 Å3/Da / Density % sol: 42.4 %
Crystal growDetails: 16% PEG3350 0.30 M K3CIT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jan 31, 2005
RadiationMonochromator: OSMIC HR MULTILAYER OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→19.9 Å / Num. obs: 154258 / % possible obs: 90.1 % / Observed criterion σ(I): 0 / Redundancy: 2.83 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.14
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 2.27 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2 / % possible all: 80.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EEP

1eep


Resolution: 2.4→40 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.914 / SU B: 18.356 / SU ML: 0.222 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.65 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2520 5.1 %RANDOM
Rwork0.196 ---
obs0.199 46582 90.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.81 Å2
Baniso -1Baniso -2Baniso -3
1-3.1 Å20 Å2-1.74 Å2
2---1.68 Å20 Å2
3----2.19 Å2
Refinement stepCycle: LAST / Resolution: 2.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9820 0 100 193 10113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02210154
X-RAY DIFFRACTIONr_bond_other_d0.0020.029250
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.96613757
X-RAY DIFFRACTIONr_angle_other_deg0.802321445
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.76751328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27124.01384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.003151679
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2861546
X-RAY DIFFRACTIONr_chiral_restr0.0710.21604
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211315
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022007
X-RAY DIFFRACTIONr_nbd_refined0.1910.22248
X-RAY DIFFRACTIONr_nbd_other0.1820.29861
X-RAY DIFFRACTIONr_nbtor_refined0.1740.24945
X-RAY DIFFRACTIONr_nbtor_other0.0850.26103
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2399
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.130.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1940.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0850.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.10436539
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.054510486
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6383655
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.509113262
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1918tight positional0.050.05
2B1918tight positional0.040.05
3C1918tight positional0.040.05
4D1918tight positional0.040.05
1A2656medium positional0.310.5
2B2656medium positional0.310.5
3C2656medium positional0.290.5
4D2656medium positional0.260.5
1A1918tight thermal0.110.5
2B1918tight thermal0.10.5
3C1918tight thermal0.10.5
4D1918tight thermal0.080.5
1A2656medium thermal0.772
2B2656medium thermal0.682
3C2656medium thermal0.662
4D2656medium thermal0.552
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.358 171
Rwork0.279 2952
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)
10.948-0.01680.08231.9150.06640.8752-0.0433-0.0689-0.05230.17240.0796-0.02090.0453-0.1441-0.0363-0.25550.00050.0299-0.08320.0115-0.07283.8383-3.1878-52.1326
20.81910.10940.37891.8086-0.31231.36050.0582-0.0121-0.0145-0.15670.0150.19680.0951-0.201-0.0732-0.0791-0.0349-0.0168-0.05530.0047-0.0525-7.0038-30.6139-84.0034
30.6772-0.36230.18911.8414-0.38071.67640.02650.05360.0349-0.0283-0.01190.06-0.0321-0.1586-0.0146-0.1089-0.02570.0242-0.0932-0.0008-0.079-1.081530.7479-78.642
40.50780.05220.52032.51630.4582.0917-0.0191-0.02020.0264-0.3674-0.02540.2323-0.2579-0.30970.04450.19280.036-0.0424-0.0065-0.0061-0.0932-13.00043.5557-110.7141
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 338
2X-RAY DIFFRACTION2B25 - 337
3X-RAY DIFFRACTION3C25 - 337
4X-RAY DIFFRACTION4D25 - 337

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