HEADER HYDROLASE, RNA BINDING PROTEIN 30-MAY-20 6X7U TITLE CRYSTAL STRUCTURE OF THE HUMAN NUDIX HYDROLASE NUDT16 IN COMPLEX WITH TITLE 2 FAD COMPND MOL_ID: 1; COMPND 2 MOLECULE: U8 SNORNA-DECAPPING ENZYME; COMPND 3 CHAIN: A, C; COMPND 4 SYNONYM: IDP PHOSPHATASE,IDPASE,INOSINE DIPHOSPHATE PHOSPHATASE, COMPND 5 NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 16,NUDIX MOTIF 16,NUDIX COMPND 6 HYDROLASE 16,U8 SNORNA-BINDING PROTEIN H29K,M7GPPPN-MRNA HYDROLASE; COMPND 7 EC: 3.6.1.62,3.6.1.64; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NUDT16; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS NUDIX, HYDROLASE, FAD, DECAPPING, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.HAMILTON,L.TONG REVDAT 3 18-OCT-23 6X7U 1 LINK REVDAT 2 22-JUL-20 6X7U 1 JRNL REVDAT 1 01-JUL-20 6X7U 0 JRNL AUTH S.SHARMA,E.GRUDZIEN-NOGALSKA,K.HAMILTON,X.JIAO,J.YANG, JRNL AUTH 2 L.TONG,M.KILEDJIAN JRNL TITL MAMMALIAN NUDIX PROTEINS CLEAVE NUCLEOTIDE METABOLITE CAPS JRNL TITL 2 ON RNAS. JRNL REF NUCLEIC ACIDS RES. V. 48 6788 2020 JRNL REFN ESSN 1362-4962 JRNL PMID 32432673 JRNL DOI 10.1093/NAR/GKAA402 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 9480 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.500 REMARK 3 FREE R VALUE TEST SET COUNT : 448 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 695 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.86 REMARK 3 BIN R VALUE (WORKING SET) : 0.3950 REMARK 3 BIN FREE R VALUE SET COUNT : 30 REMARK 3 BIN FREE R VALUE : 0.4850 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2524 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 80 REMARK 3 SOLVENT ATOMS : 36 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.01000 REMARK 3 B22 (A**2) : 2.01000 REMARK 3 B33 (A**2) : -4.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.071 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.256 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.627 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2657 ; 0.006 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2482 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3602 ; 1.498 ; 1.647 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5695 ; 1.151 ; 1.576 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 321 ; 7.727 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 161 ;28.839 ;19.255 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 425 ;18.355 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;15.161 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 319 ; 0.054 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3016 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 630 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TWIN DETAILS REMARK 3 NUMBER OF TWIN DOMAINS : 2 REMARK 3 TWIN DOMAIN : 1 REMARK 3 TWIN OPERATOR : H, K, L REMARK 3 TWIN FRACTION : 0.644 REMARK 3 TWIN DOMAIN : 2 REMARK 3 TWIN OPERATOR : K, H, -L REMARK 3 TWIN FRACTION : 0.356 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6X7U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1000249728. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-OCT-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97910 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9929 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 45.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.87 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.650 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3COU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM CHLORIDE AND 20% (W/V) REMARK 280 PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.83400 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.91700 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 GLY A 3 REMARK 465 ALA A 4 REMARK 465 ARG A 5 REMARK 465 ARG A 6 REMARK 465 LEU A 7 REMARK 465 GLU A 8 REMARK 465 LEU A 9 REMARK 465 GLY A 10 REMARK 465 GLU A 11 REMARK 465 ALA A 12 REMARK 465 LEU A 13 REMARK 465 ALA A 14 REMARK 465 LEU A 15 REMARK 465 GLY A 16 REMARK 465 SER A 17 REMARK 465 GLY A 18 REMARK 465 LEU A 181 REMARK 465 GLN A 182 REMARK 465 SER A 183 REMARK 465 GLY A 184 REMARK 465 MET C 1 REMARK 465 ALA C 2 REMARK 465 GLY C 3 REMARK 465 ALA C 4 REMARK 465 ARG C 5 REMARK 465 ARG C 6 REMARK 465 LEU C 7 REMARK 465 GLU C 8 REMARK 465 LEU C 9 REMARK 465 GLY C 10 REMARK 465 GLU C 11 REMARK 465 ALA C 12 REMARK 465 LEU C 13 REMARK 465 ALA C 14 REMARK 465 LEU C 15 REMARK 465 GLY C 16 REMARK 465 SER C 17 REMARK 465 GLY C 18 REMARK 465 TRP C 19 REMARK 465 LEU C 181 REMARK 465 GLN C 182 REMARK 465 SER C 183 REMARK 465 GLY C 184 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG A 38 -29.41 -145.13 REMARK 500 ARG A 42 -55.61 83.05 REMARK 500 LEU A 69 -55.71 -20.78 REMARK 500 ARG A 96 -61.52 -120.40 REMARK 500 ARG A 105 84.29 -48.56 REMARK 500 LEU A 135 -89.33 -112.96 REMARK 500 VAL A 152 -47.47 -134.84 REMARK 500 ASN A 161 171.17 -53.30 REMARK 500 GLN A 176 -73.78 -55.13 REMARK 500 ASP A 177 -46.59 -29.61 REMARK 500 LEU A 178 56.63 -109.85 REMARK 500 ARG C 38 -50.66 -126.77 REMARK 500 ARG C 42 -73.10 72.51 REMARK 500 THR C 64 -65.49 -26.54 REMARK 500 LEU C 73 -70.39 -62.07 REMARK 500 GLU C 83 36.78 -84.41 REMARK 500 TYR C 95 151.05 -49.82 REMARK 500 ARG C 96 -59.21 -139.26 REMARK 500 ARG C 105 -11.33 72.90 REMARK 500 LEU C 135 -98.72 -136.79 REMARK 500 VAL C 152 -42.64 -131.73 REMARK 500 LEU C 178 113.64 164.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 202 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 59 O REMARK 620 2 GLU A 80 OE2 61.2 REMARK 620 3 FAD A 201 O1A 80.1 138.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 204 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 99 NE2 REMARK 620 2 GLU A 173 OE1 84.2 REMARK 620 3 GLU A 173 OE2 134.4 50.3 REMARK 620 4 HIS C 99 NE2 74.9 77.9 95.7 REMARK 620 5 GLU C 173 OE2 71.3 80.8 100.4 4.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN C 202 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY C 59 O REMARK 620 2 GLU C 80 OE2 82.1 REMARK 620 3 AMP C 201 O2P 86.9 166.4 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FAD A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AMP C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN C 202 DBREF 6X7U A 1 184 UNP Q96DE0 NUD16_HUMAN 1 184 DBREF 6X7U C 1 184 UNP Q96DE0 NUD16_HUMAN 1 184 SEQRES 1 A 184 MET ALA GLY ALA ARG ARG LEU GLU LEU GLY GLU ALA LEU SEQRES 2 A 184 ALA LEU GLY SER GLY TRP ARG HIS ALA CYS HIS ALA LEU SEQRES 3 A 184 LEU TYR ALA PRO ASP PRO GLY MET LEU PHE GLY ARG ILE SEQRES 4 A 184 PRO LEU ARG TYR ALA ILE LEU MET GLN MET ARG PHE ASP SEQRES 5 A 184 GLY ARG LEU GLY PHE PRO GLY GLY PHE VAL ASP THR GLN SEQRES 6 A 184 ASP ARG SER LEU GLU ASP GLY LEU ASN ARG GLU LEU ARG SEQRES 7 A 184 GLU GLU LEU GLY GLU ALA ALA ALA ALA PHE ARG VAL GLU SEQRES 8 A 184 ARG THR ASP TYR ARG SER SER HIS VAL GLY SER GLY PRO SEQRES 9 A 184 ARG VAL VAL ALA HIS PHE TYR ALA LYS ARG LEU THR LEU SEQRES 10 A 184 GLU GLU LEU LEU ALA VAL GLU ALA GLY ALA THR ARG ALA SEQRES 11 A 184 LYS ASP HIS GLY LEU GLU VAL LEU GLY LEU VAL ARG VAL SEQRES 12 A 184 PRO LEU TYR THR LEU ARG ASP GLY VAL GLY GLY LEU PRO SEQRES 13 A 184 THR PHE LEU GLU ASN SER PHE ILE GLY SER ALA ARG GLU SEQRES 14 A 184 GLN LEU LEU GLU ALA LEU GLN ASP LEU GLY LEU LEU GLN SEQRES 15 A 184 SER GLY SEQRES 1 C 184 MET ALA GLY ALA ARG ARG LEU GLU LEU GLY GLU ALA LEU SEQRES 2 C 184 ALA LEU GLY SER GLY TRP ARG HIS ALA CYS HIS ALA LEU SEQRES 3 C 184 LEU TYR ALA PRO ASP PRO GLY MET LEU PHE GLY ARG ILE SEQRES 4 C 184 PRO LEU ARG TYR ALA ILE LEU MET GLN MET ARG PHE ASP SEQRES 5 C 184 GLY ARG LEU GLY PHE PRO GLY GLY PHE VAL ASP THR GLN SEQRES 6 C 184 ASP ARG SER LEU GLU ASP GLY LEU ASN ARG GLU LEU ARG SEQRES 7 C 184 GLU GLU LEU GLY GLU ALA ALA ALA ALA PHE ARG VAL GLU SEQRES 8 C 184 ARG THR ASP TYR ARG SER SER HIS VAL GLY SER GLY PRO SEQRES 9 C 184 ARG VAL VAL ALA HIS PHE TYR ALA LYS ARG LEU THR LEU SEQRES 10 C 184 GLU GLU LEU LEU ALA VAL GLU ALA GLY ALA THR ARG ALA SEQRES 11 C 184 LYS ASP HIS GLY LEU GLU VAL LEU GLY LEU VAL ARG VAL SEQRES 12 C 184 PRO LEU TYR THR LEU ARG ASP GLY VAL GLY GLY LEU PRO SEQRES 13 C 184 THR PHE LEU GLU ASN SER PHE ILE GLY SER ALA ARG GLU SEQRES 14 C 184 GLN LEU LEU GLU ALA LEU GLN ASP LEU GLY LEU LEU GLN SEQRES 15 C 184 SER GLY HET FAD A 201 53 HET MN A 202 1 HET MN A 203 1 HET MN A 204 1 HET AMP C 201 23 HET MN C 202 1 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM MN MANGANESE (II) ION HETNAM AMP ADENOSINE MONOPHOSPHATE FORMUL 3 FAD C27 H33 N9 O15 P2 FORMUL 4 MN 4(MN 2+) FORMUL 7 AMP C10 H14 N5 O7 P FORMUL 9 HOH *36(H2 O) HELIX 1 AA1 PHE A 36 ARG A 38 5 3 HELIX 2 AA2 SER A 68 GLY A 82 1 15 HELIX 3 AA3 GLU A 83 PHE A 88 5 6 HELIX 4 AA4 GLU A 91 THR A 93 5 3 HELIX 5 AA5 THR A 116 ALA A 127 1 12 HELIX 6 AA6 GLY A 154 LEU A 159 1 6 HELIX 7 AA7 SER A 166 LEU A 178 1 13 HELIX 8 AA8 PHE C 36 ARG C 38 5 3 HELIX 9 AA9 SER C 68 GLY C 82 1 15 HELIX 10 AB1 GLU C 91 THR C 93 5 3 HELIX 11 AB2 THR C 116 ALA C 127 1 12 HELIX 12 AB3 GLY C 154 LEU C 159 1 6 HELIX 13 AB4 SER C 166 LEU C 178 1 13 SHEET 1 AA1 5 LEU A 55 GLY A 56 0 SHEET 2 AA1 5 ILE A 39 ARG A 50 -1 N GLN A 48 O GLY A 56 SHEET 3 AA1 5 HIS A 21 LEU A 35 -1 N ALA A 29 O ALA A 44 SHEET 4 AA1 5 VAL A 106 ARG A 114 1 O HIS A 109 N ALA A 22 SHEET 5 AA1 5 TYR A 95 GLY A 101 -1 N GLY A 101 O VAL A 106 SHEET 1 AA2 4 GLY A 59 PHE A 61 0 SHEET 2 AA2 4 HIS A 21 LEU A 35 -1 N CYS A 23 O GLY A 60 SHEET 3 AA2 4 ILE A 39 ARG A 50 -1 O ALA A 44 N ALA A 29 SHEET 4 AA2 4 VAL A 137 ARG A 142 -1 O VAL A 141 N MET A 47 SHEET 1 AA3 5 LEU C 55 GLY C 56 0 SHEET 2 AA3 5 ILE C 39 ARG C 50 -1 N GLN C 48 O GLY C 56 SHEET 3 AA3 5 HIS C 21 LEU C 35 -1 N LEU C 35 O ILE C 39 SHEET 4 AA3 5 VAL C 107 ARG C 114 1 O HIS C 109 N ALA C 22 SHEET 5 AA3 5 TYR C 95 VAL C 100 -1 N SER C 97 O PHE C 110 SHEET 1 AA4 4 GLY C 59 PHE C 61 0 SHEET 2 AA4 4 HIS C 21 LEU C 35 -1 N CYS C 23 O GLY C 60 SHEET 3 AA4 4 ILE C 39 ARG C 50 -1 O ILE C 39 N LEU C 35 SHEET 4 AA4 4 VAL C 137 ARG C 142 -1 O VAL C 141 N MET C 47 LINK O GLY A 59 MN MN A 202 1555 1555 2.29 LINK OE2 GLU A 80 MN MN A 202 1555 1555 2.17 LINK NE2 HIS A 99 MN MN A 204 1555 1555 2.43 LINK OE1 GLU A 173 MN MN A 204 1555 1555 2.69 LINK OE2 GLU A 173 MN MN A 204 1555 1555 2.56 LINK O1A FAD A 201 MN MN A 202 1555 1555 2.05 LINK MN MN A 204 NE2 HIS C 99 3565 1555 2.06 LINK MN MN A 204 OE2 GLU C 173 3565 1555 2.25 LINK O GLY C 59 MN MN C 202 1555 1555 2.05 LINK OE2 GLU C 80 MN MN C 202 1555 1555 2.35 LINK O2P AMP C 201 MN MN C 202 1555 1555 2.26 SITE 1 AC1 24 ALA A 22 HIS A 24 ARG A 50 PHE A 51 SITE 2 AC1 24 GLY A 56 PHE A 57 GLY A 59 GLY A 60 SITE 3 AC1 24 PHE A 61 ALA A 86 ALA A 87 PHE A 88 SITE 4 AC1 24 VAL A 106 ILE A 164 ALA A 167 GLN A 170 SITE 5 AC1 24 MN A 202 MN A 203 HOH A 301 HOH A 304 SITE 6 AC1 24 HOH A 312 PHE C 36 ARG C 38 LEU C 148 SITE 1 AC2 3 GLY A 59 GLU A 80 FAD A 201 SITE 1 AC3 2 GLU A 76 FAD A 201 SITE 1 AC4 4 HIS A 99 GLU A 173 HIS C 99 GLU C 173 SITE 1 AC5 11 HIS C 24 ARG C 50 GLY C 56 PHE C 57 SITE 2 AC5 11 GLY C 59 GLY C 60 PHE C 61 ILE C 164 SITE 3 AC5 11 GLN C 170 MN C 202 HOH C 301 SITE 1 AC6 4 GLY C 59 GLY C 60 GLU C 80 AMP C 201 CRYST1 64.721 64.721 77.751 90.00 90.00 120.00 P 32 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.015451 0.008921 0.000000 0.00000 SCALE2 0.000000 0.017841 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012862 0.00000