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- PDB-5c3z: Crystal structure of human ribokinase in complex with AMPPCP in C... -

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Basic information

Entry
Database: PDB / ID: 5c3z
TitleCrystal structure of human ribokinase in complex with AMPPCP in C2 spacegroup
ComponentsRibokinase
KeywordsTRANSFERASE
Function / homology
Function and homology information


ribokinase / ribokinase activity / Pentose phosphate pathway / D-ribose catabolic process / pentose-phosphate shunt / ATP binding / identical protein binding / nucleus / metal ion binding / cytosol
Similarity search - Function
Ribokinase / Ribokinase/fructokinase / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Ribokinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPark, J. / Chakrabarti, J. / Singh, B. / Gupta, R.S. / Junop, M.S.
CitationJournal: To Be Published
Title: Crystal structure of human ribokinase in complex with AMPPCP in C2 spacegroup
Authors: Park, J. / Chakrabarti, J. / Singh, B. / Gupta, R.S. / Junop, M.S.
History
DepositionJun 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references / Structure summary
Revision 1.2Sep 27, 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_ncs_dom_lim
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_alt_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_seq_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_alt_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.pdbx_ptnr2_label_alt_id / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribokinase
B: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,69111
Polymers70,4822
Non-polymers1,2099
Water9,152508
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-21 kcal/mol
Surface area26270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.557, 72.943, 91.864
Angle α, β, γ (deg.)90.00, 114.81, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 11 - 324 / Label seq-ID: 11 - 324

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Ribokinase


Mass: 35241.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBKS, RBSK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H477, ribokinase
#2: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 508 / 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: 60.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M sodium HEPES, 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 67611 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 18.464
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 2.875 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FV7

2fv7


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.96 / SU B: 5.181 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18766 3427 5.1 %RANDOM
Rwork0.14934 ---
obs0.15125 64182 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.267 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å2-0.11 Å2
2--1.16 Å20 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4651 0 69 508 5228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0194892
X-RAY DIFFRACTIONr_bond_other_d0.0120.024636
X-RAY DIFFRACTIONr_angle_refined_deg2.4351.9816694
X-RAY DIFFRACTIONr_angle_other_deg1.817310666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0115655
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.01625.611180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13615778
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5581515
X-RAY DIFFRACTIONr_chiral_restr0.1540.2812
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.025638
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021037
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.711.9322590
X-RAY DIFFRACTIONr_mcbond_other1.711.9312589
X-RAY DIFFRACTIONr_mcangle_it2.3072.8823255
X-RAY DIFFRACTIONr_mcangle_other2.3072.8833256
X-RAY DIFFRACTIONr_scbond_it2.8232.3192302
X-RAY DIFFRACTIONr_scbond_other2.8232.322303
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2443.3563440
X-RAY DIFFRACTIONr_long_range_B_refined7.58518.235762
X-RAY DIFFRACTIONr_long_range_B_other7.58518.2345763
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 35892 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.894→1.943 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 242 -
Rwork0.227 4446 -
obs--93.8 %
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)
19.4095.87453.66123.70662.30491.48550.13490.10780.02370.14050.0096-0.06510.03740.0822-0.14450.228-0.0356-0.00510.2742-0.0190.420361.78559.342117.2885
27.1406-2.784-6.5021.77841.80246.6957-0.18160.7415-0.10460.15060.0271-0.01360.0911-1.00380.15450.10780.0590.00630.2395-0.03570.027330.351111.82119.8977
31.8861-1.4394-0.98061.9296-0.07622.3019-0.0895-0.09080.22240.1290.1155-0.055-0.0988-0.0521-0.02610.09480.0675-0.02120.0485-0.01640.084235.253214.413618.5665
42.21010.6470.60313.490.84061.8888-0.10130.22410.051-0.28360.02920.07850.00420.09850.07210.10450.04640.01610.05920.01990.009540.92590.52583.4457
54.9285-1.2288-3.81782.90832.437110.4046-0.1841-0.1213-0.61790.0443-0.1212-0.0290.7040.02480.30530.17250.02670.02960.02480.01690.129437.9818-14.302310.4456
66.2060.8617-0.93032.38440.33713.2567-0.0257-0.3817-0.30750.1977-0.0461-0.14930.44120.12580.07170.12820.07960.01340.10560.03770.02543.8308-5.372722.6457
75.2305-0.80941.16493.25426.115113.2403-0.0570.26380.11620.01590.0215-0.05170.18690.2960.03550.1863-0.02840.01530.18040.01370.216422.150854.676945.8448
82.4862-2.5673-3.93282.98143.3317.8568-0.06150.15330.00060.0045-0.1319-0.06920.252-0.26790.19340.04370.04760.02240.11340.00660.119919.004429.644126.1235
91.6634-1.0381-1.17812.54740.38563.12270.13720.0120.1113-0.1199-0.0485-0.3117-0.10340.1694-0.08870.04330.03920.03650.06490.0410.090622.909829.170727.4552
102.7514-1.0622-0.73022.3640.41152.18330.1316-0.13820.02590.15190.006-0.0375-0.0698-0.2004-0.13760.09230.04250.02160.0730.03270.027610.054930.785538.5526
114.27250.36190.89413.578-0.0394.12960.07720.22070.1180.07730.02490.2671-0.1985-0.4396-0.10210.09690.15070.0450.24750.07240.0765-6.359534.172429.1656
124.02730.84250.93543.01760.25654.2484-0.02690.48380.5422-0.21690.09290.0408-0.5805-0.1928-0.0660.21440.11720.06830.13930.12210.13088.888444.74923.2122
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 18
2X-RAY DIFFRACTION2A19 - 34
3X-RAY DIFFRACTION3A35 - 135
4X-RAY DIFFRACTION4A136 - 233
5X-RAY DIFFRACTION5A234 - 257
6X-RAY DIFFRACTION6A258 - 326
7X-RAY DIFFRACTION7B10 - 14
8X-RAY DIFFRACTION8B15 - 34
9X-RAY DIFFRACTION9B35 - 114
10X-RAY DIFFRACTION10B115 - 200
11X-RAY DIFFRACTION11B201 - 257
12X-RAY DIFFRACTION12B258 - 325

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