HEADER TRANSFERASE 08-FEB-22 7R4L TITLE CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL NAD KINASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAD KINASE 2, MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 SYNONYM: MITOCHONDRIAL NAD KINASE,NAD KINASE DOMAIN-CONTAINING COMPND 6 PROTEIN 1,MITOCHONDRIAL; COMPND 7 EC: 2.7.1.23; 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: NADK2, C5ORF33, MNADK, NADKD1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS NADP BOUND FORM WITH IRON, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR G.LABESSE,C.MARY,M.GELIN,C.LIONNE REVDAT 4 01-MAY-24 7R4L 1 REMARK REVDAT 3 14-SEP-22 7R4L 1 JRNL REVDAT 2 03-AUG-22 7R4L 1 JRNL REVDAT 1 06-JUL-22 7R4L 0 JRNL AUTH C.MARY,M.H.SOFLAEE,R.KESAVAN,M.GELIN,H.BROWN,G.ZACHARIAS, JRNL AUTH 2 T.P.MATHEWS,A.LEMOFF,C.LIONNE,G.LABESSE,G.HOXHAJ JRNL TITL CRYSTAL STRUCTURE OF HUMAN NADK2 REVEALS A DIMERIC JRNL TITL 2 ORGANIZATION AND ACTIVE SITE OCCLUSION BY LYSINE JRNL TITL 3 ACETYLATION. JRNL REF MOL.CELL V. 82 3299 2022 JRNL REFN ISSN 1097-2765 JRNL PMID 35868311 JRNL DOI 10.1016/J.MOLCEL.2022.06.026 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 17069 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 860 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 48.3700 - 4.7200 0.98 2869 153 0.1854 0.2115 REMARK 3 2 4.7200 - 3.7500 1.00 2707 142 0.1369 0.1795 REMARK 3 3 3.7500 - 3.2800 1.00 2670 160 0.1744 0.2612 REMARK 3 4 3.2800 - 2.9800 1.00 2663 142 0.1954 0.2774 REMARK 3 5 2.9800 - 2.7600 1.00 2642 139 0.2088 0.2812 REMARK 3 6 2.7600 - 2.6000 1.00 2658 124 0.2304 0.3127 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.322 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.687 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.13 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 2759 REMARK 3 ANGLE : 1.062 3746 REMARK 3 CHIRALITY : 0.088 415 REMARK 3 PLANARITY : 0.008 483 REMARK 3 DIHEDRAL : 17.452 1015 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 64 THROUGH 109 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.9511 -5.5421 23.3494 REMARK 3 T TENSOR REMARK 3 T11: 0.3193 T22: 0.4852 REMARK 3 T33: 0.4188 T12: 0.0426 REMARK 3 T13: 0.0951 T23: 0.0961 REMARK 3 L TENSOR REMARK 3 L11: 5.5261 L22: 5.8822 REMARK 3 L33: 5.4301 L12: -0.8887 REMARK 3 L13: 1.4299 L23: -0.7315 REMARK 3 S TENSOR REMARK 3 S11: 0.2363 S12: 0.6748 S13: 0.5694 REMARK 3 S21: -0.6167 S22: -0.0146 S23: 0.1058 REMARK 3 S31: -0.6657 S32: 0.2546 S33: 0.1004 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 110 THROUGH 221 ) REMARK 3 ORIGIN FOR THE GROUP (A): -22.6133 -15.8020 30.5441 REMARK 3 T TENSOR REMARK 3 T11: 0.1839 T22: 0.3823 REMARK 3 T33: 0.3038 T12: -0.0271 REMARK 3 T13: 0.0016 T23: 0.0574 REMARK 3 L TENSOR REMARK 3 L11: 2.5823 L22: 1.9058 REMARK 3 L33: 2.6502 L12: -0.6001 REMARK 3 L13: -0.5682 L23: 0.9658 REMARK 3 S TENSOR REMARK 3 S11: 0.0186 S12: -0.3273 S13: 0.0898 REMARK 3 S21: 0.1319 S22: 0.0838 S23: -0.0071 REMARK 3 S31: 0.0023 S32: 0.0548 S33: -0.1016 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 222 THROUGH 327 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.7644 -27.8984 7.2115 REMARK 3 T TENSOR REMARK 3 T11: 0.2468 T22: 0.2414 REMARK 3 T33: 0.3265 T12: -0.0002 REMARK 3 T13: -0.0144 T23: 0.0275 REMARK 3 L TENSOR REMARK 3 L11: 1.9934 L22: 1.7422 REMARK 3 L33: 3.4225 L12: -0.1590 REMARK 3 L13: 0.0676 L23: 0.1300 REMARK 3 S TENSOR REMARK 3 S11: -0.0149 S12: 0.0681 S13: -0.1701 REMARK 3 S21: -0.2052 S22: 0.1325 S23: -0.1053 REMARK 3 S31: 0.4241 S32: 0.2805 S33: -0.0986 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 328 THROUGH 349 ) REMARK 3 ORIGIN FOR THE GROUP (A): -45.1601 -37.0227 -2.0211 REMARK 3 T TENSOR REMARK 3 T11: 0.5387 T22: 1.0396 REMARK 3 T33: 0.8353 T12: -0.4128 REMARK 3 T13: -0.2460 T23: 0.1678 REMARK 3 L TENSOR REMARK 3 L11: 2.6437 L22: 1.0231 REMARK 3 L33: 0.2766 L12: 0.1996 REMARK 3 L13: -0.7583 L23: 0.0227 REMARK 3 S TENSOR REMARK 3 S11: -0.1463 S12: 0.2115 S13: -0.0069 REMARK 3 S21: -0.1554 S22: -0.2066 S23: 0.6521 REMARK 3 S31: 0.2247 S32: -0.5659 S33: 0.0150 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 350 THROUGH 377 ) REMARK 3 ORIGIN FOR THE GROUP (A): -31.5330 -35.2445 11.6605 REMARK 3 T TENSOR REMARK 3 T11: 0.3246 T22: 0.6037 REMARK 3 T33: 0.5304 T12: -0.1604 REMARK 3 T13: -0.0475 T23: 0.1681 REMARK 3 L TENSOR REMARK 3 L11: 2.3095 L22: 1.4121 REMARK 3 L33: 1.1027 L12: 1.1103 REMARK 3 L13: 0.9351 L23: 1.2409 REMARK 3 S TENSOR REMARK 3 S11: 0.1732 S12: -0.1189 S13: 0.1002 REMARK 3 S21: -0.0854 S22: 0.0242 S23: 0.5177 REMARK 3 S31: 0.3870 S32: -1.0185 S33: -0.0350 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 378 THROUGH 402 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.1952 -35.6915 0.1117 REMARK 3 T TENSOR REMARK 3 T11: 0.5714 T22: 0.3378 REMARK 3 T33: 0.5204 T12: -0.0167 REMARK 3 T13: -0.0583 T23: -0.0698 REMARK 3 L TENSOR REMARK 3 L11: 2.8013 L22: 1.3183 REMARK 3 L33: 4.6160 L12: 0.4869 REMARK 3 L13: -1.1399 L23: -1.0152 REMARK 3 S TENSOR REMARK 3 S11: -0.0068 S12: 0.5906 S13: -0.7339 REMARK 3 S21: -0.5164 S22: 0.2024 S23: 0.0979 REMARK 3 S31: 1.0707 S32: -0.1790 S33: -0.0077 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 403 THROUGH 441 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.4214 -26.7185 13.5066 REMARK 3 T TENSOR REMARK 3 T11: 0.1761 T22: 0.2692 REMARK 3 T33: 0.3282 T12: 0.0225 REMARK 3 T13: -0.0391 T23: 0.0166 REMARK 3 L TENSOR REMARK 3 L11: 2.0846 L22: 1.6524 REMARK 3 L33: 6.8887 L12: 0.5474 REMARK 3 L13: -1.9494 L23: -0.4823 REMARK 3 S TENSOR REMARK 3 S11: -0.0842 S12: -0.1119 S13: -0.2312 REMARK 3 S21: -0.0827 S22: 0.0408 S23: -0.0530 REMARK 3 S31: 0.1916 S32: 0.3902 S33: -0.0136 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7R4L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1292120912. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-SEP-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID30B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.7 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17069 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 48.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.51700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 1.3600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.61 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 1.05100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: ALPHAFOLD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 400 28% V/V, CACL2 150 MM, 0.1 M REMARK 280 SODIUM HEPES, 2% GLYCEROL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 111.61200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.20300 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.20300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 167.41800 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.20300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.20300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 55.80600 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.20300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.20300 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 167.41800 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.20300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.20300 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 55.80600 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 111.61200 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: 6840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 679 LIES ON A SPECIAL POSITION. 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 52 REMARK 465 GLY A 53 REMARK 465 HIS A 54 REMARK 465 HIS A 55 REMARK 465 HIS A 56 REMARK 465 HIS A 57 REMARK 465 HIS A 58 REMARK 465 HIS A 59 REMARK 465 GLY A 60 REMARK 465 ARG A 61 REMARK 465 ALA A 62 REMARK 465 ASP A 63 REMARK 465 ARG A 88 REMARK 465 TYR A 89 REMARK 465 ALA A 90 REMARK 465 GLU A 91 REMARK 465 LEU A 92 REMARK 465 SER A 93 REMARK 465 GLU A 94 REMARK 465 GLU A 95 REMARK 465 ASP A 96 REMARK 465 LEU A 97 REMARK 465 LYS A 98 REMARK 465 GLN A 99 REMARK 465 LEU A 100 REMARK 465 LEU A 101 REMARK 465 GLN A 241 REMARK 465 GLN A 242 REMARK 465 LEU A 243 REMARK 465 SER A 244 REMARK 465 LEU A 245 REMARK 465 ASN A 246 REMARK 465 GLN A 247 REMARK 465 HIS A 248 REMARK 465 ASN A 249 REMARK 465 ARG A 250 REMARK 465 ALA A 251 REMARK 465 LEU A 252 REMARK 465 ASN A 253 REMARK 465 ILE A 254 REMARK 465 GLU A 255 REMARK 465 ARG A 256 REMARK 465 ALA A 257 REMARK 465 HIS A 258 REMARK 465 ASP A 259 REMARK 465 GLU A 260 REMARK 465 ARG A 261 REMARK 465 SER A 262 REMARK 465 GLU A 263 REMARK 465 GLY A 342 REMARK 465 ASN A 343 REMARK 465 LEU A 344 REMARK 465 SER A 345 REMARK 465 GLN A 442 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 TYR A 87 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU A 103 CG CD1 CD2 REMARK 470 LYS A 104 CG CD CE NZ REMARK 470 TYR A 108 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 339 CG CD CE NZ REMARK 470 ARG A 340 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 341 CG CD OE1 NE2 REMARK 470 LEU A 346 CG CD1 CD2 REMARK 470 LEU A 348 CG CD1 CD2 REMARK 470 GLU A 351 CG CD OE1 OE2 REMARK 470 LYS A 355 CG CD CE NZ REMARK 470 ARG A 384 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 386 CG CD1 CD2 CE1 CE2 CZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OH TYR A 291 OG SER A 305 2.14 REMARK 500 O TYR A 360 OG SER A 363 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 730 O HOH A 751 6445 2.13 REMARK 500 O HOH A 703 O HOH A 748 6545 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASN A 349 CA - C - N ANGL. DEV. = -14.9 DEGREES REMARK 500 ASN A 349 O - C - N ANGL. DEV. = 13.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 PHE A 66 108.93 -167.08 REMARK 500 ARG A 86 -7.94 -169.91 REMARK 500 LYS A 104 -86.17 -69.93 REMARK 500 SER A 106 -96.04 -86.21 REMARK 500 SER A 107 73.57 -65.58 REMARK 500 TYR A 108 -91.25 -67.93 REMARK 500 ARG A 141 -60.81 -29.17 REMARK 500 ASN A 276 -68.64 -96.08 REMARK 500 ALA A 318 -133.47 -90.15 REMARK 500 ARG A 340 -70.70 -72.19 REMARK 500 ARG A 350 -35.77 -34.05 REMARK 500 ALA A 382 -101.71 -87.54 REMARK 500 ASN A 383 -167.39 64.13 REMARK 500 SER A 389 -121.65 -90.22 REMARK 500 ASP A 406 67.73 -150.99 REMARK 500 PHE A 419 75.03 -152.55 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 FE A 502 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 NAP A 501 O1A REMARK 620 2 NAP A 501 O1N 74.4 REMARK 620 3 NAP A 501 O3X 100.3 87.9 REMARK 620 4 HOH A 719 O 169.5 95.4 81.5 REMARK 620 N 1 2 3 DBREF 7R4L A 61 442 UNP Q4G0N4 NAKD2_HUMAN 61 442 SEQADV 7R4L MET A 52 UNP Q4G0N4 INITIATING METHIONINE SEQADV 7R4L GLY A 53 UNP Q4G0N4 EXPRESSION TAG SEQADV 7R4L HIS A 54 UNP Q4G0N4 EXPRESSION TAG SEQADV 7R4L HIS A 55 UNP Q4G0N4 EXPRESSION TAG SEQADV 7R4L HIS A 56 UNP Q4G0N4 EXPRESSION TAG SEQADV 7R4L HIS A 57 UNP Q4G0N4 EXPRESSION TAG SEQADV 7R4L HIS A 58 UNP Q4G0N4 EXPRESSION TAG SEQADV 7R4L HIS A 59 UNP Q4G0N4 EXPRESSION TAG SEQADV 7R4L GLY A 60 UNP Q4G0N4 EXPRESSION TAG SEQRES 1 A 391 MET GLY HIS HIS HIS HIS HIS HIS GLY ARG ALA ASP GLY SEQRES 2 A 391 GLY PHE ARG PRO SER ARG VAL VAL VAL VAL ALA LYS THR SEQRES 3 A 391 THR ARG TYR GLU PHE GLU GLN GLN ARG TYR ARG TYR ALA SEQRES 4 A 391 GLU LEU SER GLU GLU ASP LEU LYS GLN LEU LEU ALA LEU SEQRES 5 A 391 LYS GLY SER SER TYR SER GLY LEU LEU GLU ARG HIS HIS SEQRES 6 A 391 ILE HIS THR LYS ASN VAL GLU HIS ILE ILE ASP SER LEU SEQRES 7 A 391 ARG ASN GLU GLY ILE GLU VAL ARG LEU VAL LYS ARG ARG SEQRES 8 A 391 GLU TYR ASP GLU GLU THR VAL ARG TRP ALA ASP ALA VAL SEQRES 9 A 391 ILE ALA ALA GLY GLY ASP GLY THR MET LEU LEU ALA ALA SEQRES 10 A 391 SER LYS VAL LEU ASP ARG LEU LYS PRO VAL ILE GLY VAL SEQRES 11 A 391 ASN THR ASP PRO GLU ARG SER GLU GLY HIS LEU CYS LEU SEQRES 12 A 391 PRO VAL ARG TYR THR HIS SER PHE PRO GLU ALA LEU GLN SEQRES 13 A 391 LYS PHE TYR ARG GLY GLU PHE ARG TRP LEU TRP ARG GLN SEQRES 14 A 391 ARG ILE ARG LEU TYR LEU GLU GLY THR GLY ILE ASN PRO SEQRES 15 A 391 VAL PRO VAL ASP LEU HIS GLU GLN GLN LEU SER LEU ASN SEQRES 16 A 391 GLN HIS ASN ARG ALA LEU ASN ILE GLU ARG ALA HIS ASP SEQRES 17 A 391 GLU ARG SER GLU ALA SER GLY PRO GLN LEU LEU PRO VAL SEQRES 18 A 391 ARG ALA LEU ASN GLU VAL PHE ILE GLY GLU SER LEU SER SEQRES 19 A 391 SER ARG ALA SER TYR TYR GLU ILE SER VAL ASP ASP GLY SEQRES 20 A 391 PRO TRP GLU LYS GLN LYS SER SER GLY LEU ASN LEU CYS SEQRES 21 A 391 THR GLY THR GLY SER LYS ALA TRP SER PHE ASN ILE ASN SEQRES 22 A 391 ARG VAL ALA THR GLN ALA VAL GLU ASP VAL LEU ASN ILE SEQRES 23 A 391 ALA LYS ARG GLN GLY ASN LEU SER LEU PRO LEU ASN ARG SEQRES 24 A 391 GLU LEU VAL GLU LYS VAL THR ASN GLU TYR ASN GLU SER SEQRES 25 A 391 LEU LEU TYR SER PRO GLU GLU PRO LYS ILE LEU PHE SER SEQRES 26 A 391 ILE ARG GLU PRO ILE ALA ASN ARG VAL PHE SER SER SER SEQRES 27 A 391 ARG GLN ARG CYS PHE SER SER LYS VAL CYS VAL ARG SER SEQRES 28 A 391 ARG CYS TRP ASP ALA CYS MET VAL VAL ASP GLY GLY THR SEQRES 29 A 391 SER PHE GLU PHE ASN ASP GLY ALA ILE ALA SER MET MET SEQRES 30 A 391 ILE ASN LYS GLU ASP GLU LEU ARG THR VAL LEU LEU GLU SEQRES 31 A 391 GLN HET NAP A 501 48 HET FE A 502 1 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM FE FE (III) ION HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 2 NAP C21 H28 N7 O17 P3 FORMUL 3 FE FE 3+ FORMUL 4 HOH *165(H2 O) HELIX 1 AA1 THR A 78 GLN A 85 1 8 HELIX 2 AA2 SER A 109 GLU A 132 1 24 HELIX 3 AA3 LYS A 140 TYR A 144 5 5 HELIX 4 AA4 ASP A 145 ALA A 152 1 8 HELIX 5 AA5 GLY A 160 LYS A 170 1 11 HELIX 6 AA6 PRO A 195 HIS A 200 5 6 HELIX 7 AA7 SER A 201 ARG A 211 1 11 HELIX 8 AA8 THR A 314 LYS A 317 5 4 HELIX 9 AA9 ALA A 318 ARG A 325 1 8 HELIX 10 AB1 ALA A 327 GLN A 341 1 15 HELIX 11 AB2 ASN A 349 SER A 363 1 15 HELIX 12 AB3 LYS A 431 GLU A 434 5 4 SHEET 1 AA1 4 GLU A 135 VAL A 139 0 SHEET 2 AA1 4 ARG A 70 ALA A 75 1 N VAL A 73 O VAL A 139 SHEET 3 AA1 4 ALA A 154 GLY A 159 1 O ALA A 158 N VAL A 74 SHEET 4 AA1 4 VAL A 178 ASN A 182 1 O VAL A 181 N ALA A 157 SHEET 1 AA2 2 ARG A 215 ARG A 219 0 SHEET 2 AA2 2 LEU A 435 LEU A 439 -1 O THR A 437 N LEU A 217 SHEET 1 AA3 6 SER A 265 ALA A 274 0 SHEET 2 AA3 6 ILE A 222 GLY A 228 -1 N LEU A 224 O LEU A 270 SHEET 3 AA3 6 ALA A 423 ILE A 429 -1 O ILE A 424 N GLU A 227 SHEET 4 AA3 6 LYS A 397 SER A 402 -1 N SER A 402 O ALA A 423 SHEET 5 AA3 6 SER A 289 VAL A 295 -1 N GLU A 292 O ARG A 401 SHEET 6 AA3 6 GLU A 301 SER A 305 -1 O SER A 305 N SER A 289 SHEET 1 AA4 7 VAL A 236 ASP A 237 0 SHEET 2 AA4 7 THR A 415 GLU A 418 -1 O SER A 416 N VAL A 236 SHEET 3 AA4 7 ALA A 407 VAL A 411 -1 N VAL A 411 O THR A 415 SHEET 4 AA4 7 GLU A 277 GLU A 282 -1 N PHE A 279 O VAL A 410 SHEET 5 AA4 7 LEU A 308 CYS A 311 -1 O LEU A 310 N VAL A 278 SHEET 6 AA4 7 ILE A 373 ILE A 377 -1 O SER A 376 N ASN A 309 SHEET 7 AA4 7 ARG A 392 SER A 395 -1 O SER A 395 N ILE A 373 LINK O1A NAP A 501 FE FE A 502 1555 1555 2.36 LINK O1N NAP A 501 FE FE A 502 1555 1555 2.52 LINK O3X NAP A 501 FE FE A 502 1555 1555 2.38 LINK FE FE A 502 O HOH A 719 1555 1555 2.68 CRYST1 68.406 68.406 223.224 90.00 90.00 90.00 P 43 21 2 8 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 0.014619 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014619 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004480 0.00000