HEADER TRANSFERASE 08-FEB-22 7R4J 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 SYNONYM: MITOCHONDRIAL NAD KINASE,NAD KINASE DOMAIN-CONTAINING COMPND 5 PROTEIN 1,MITOCHONDRIAL; COMPND 6 EC: 2.7.1.23; COMPND 7 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 APO-FORM, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR G.LABESSE,C.MARY,M.GELIN,C.LIONNE REVDAT 4 01-MAY-24 7R4J 1 REMARK REVDAT 3 14-SEP-22 7R4J 1 JRNL REVDAT 2 03-AUG-22 7R4J 1 JRNL REVDAT 1 06-JUL-22 7R4J 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. 2.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.900 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 20057 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.238 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.298 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.820 REMARK 3 FREE R VALUE TEST SET COUNT : 1969 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 48.4200 - 7.1100 0.88 1203 146 0.1946 0.2436 REMARK 3 2 7.0900 - 5.6300 0.92 1250 133 0.2288 0.3009 REMARK 3 3 5.6300 - 4.9200 0.94 1281 132 0.1865 0.2796 REMARK 3 4 4.9200 - 4.4700 0.93 1297 128 0.1743 0.2319 REMARK 3 5 4.4700 - 4.1500 0.95 1287 159 0.1951 0.2993 REMARK 3 6 4.1500 - 3.9100 0.94 1292 146 0.2209 0.3573 REMARK 3 7 3.9100 - 3.7100 0.94 1294 129 0.2408 0.2897 REMARK 3 8 3.7100 - 3.5500 0.95 1269 176 0.2688 0.3309 REMARK 3 9 3.5500 - 3.4100 0.97 1324 130 0.3039 0.3061 REMARK 3 10 3.4100 - 3.3000 0.95 1344 119 0.3162 0.3394 REMARK 3 11 3.3000 - 3.1900 0.95 1311 159 0.3346 0.4147 REMARK 3 12 3.1900 - 3.1000 0.97 1293 141 0.3587 0.4260 REMARK 3 13 3.1000 - 3.0200 0.96 1333 135 0.4039 0.4408 REMARK 3 14 3.0200 - 2.9500 0.95 1310 136 0.4332 0.5051 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) : 0.630 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.970 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 100.8 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 106.5 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 64 THROUGH 110 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.5099 -4.1742 20.6152 REMARK 3 T TENSOR REMARK 3 T11: 0.7163 T22: 0.8647 REMARK 3 T33: 0.8985 T12: 0.0377 REMARK 3 T13: 0.1301 T23: 0.3375 REMARK 3 L TENSOR REMARK 3 L11: 5.3113 L22: 4.0194 REMARK 3 L33: 5.0627 L12: -2.5617 REMARK 3 L13: 0.3387 L23: -2.2199 REMARK 3 S TENSOR REMARK 3 S11: 0.9223 S12: 0.8067 S13: 0.4673 REMARK 3 S21: -0.3730 S22: 0.1741 S23: 0.1407 REMARK 3 S31: -0.2001 S32: 0.0923 S33: 0.0042 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 111 THROUGH 160 ) REMARK 3 ORIGIN FOR THE GROUP (A): -22.5904 -8.9659 30.3712 REMARK 3 T TENSOR REMARK 3 T11: 0.6670 T22: 0.7750 REMARK 3 T33: 0.8484 T12: -0.0778 REMARK 3 T13: 0.0487 T23: -0.0108 REMARK 3 L TENSOR REMARK 3 L11: 6.4454 L22: 2.9917 REMARK 3 L33: 5.5782 L12: 1.0126 REMARK 3 L13: 0.8819 L23: 0.0826 REMARK 3 S TENSOR REMARK 3 S11: 0.0707 S12: -0.1168 S13: 0.4939 REMARK 3 S21: -0.1961 S22: 0.0830 S23: -0.2682 REMARK 3 S31: -0.5687 S32: 0.7104 S33: -0.2052 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 161 THROUGH 211 ) REMARK 3 ORIGIN FOR THE GROUP (A): -28.0950 -19.0243 30.0654 REMARK 3 T TENSOR REMARK 3 T11: 0.5103 T22: 0.6587 REMARK 3 T33: 0.6515 T12: 0.0548 REMARK 3 T13: -0.0190 T23: 0.1138 REMARK 3 L TENSOR REMARK 3 L11: 3.4124 L22: 2.7830 REMARK 3 L33: 3.6359 L12: 0.7917 REMARK 3 L13: 0.1845 L23: 2.0562 REMARK 3 S TENSOR REMARK 3 S11: -0.1309 S12: 0.0924 S13: 0.1251 REMARK 3 S21: 0.3473 S22: 0.1241 S23: 0.2766 REMARK 3 S31: -0.0615 S32: -0.4554 S33: -0.0568 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 212 THROUGH 277 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.0548 -26.8902 18.7983 REMARK 3 T TENSOR REMARK 3 T11: 0.4949 T22: 0.6060 REMARK 3 T33: 0.7677 T12: 0.0688 REMARK 3 T13: -0.0543 T23: 0.0382 REMARK 3 L TENSOR REMARK 3 L11: 3.1786 L22: 4.3295 REMARK 3 L33: 5.6061 L12: 0.9404 REMARK 3 L13: -2.2835 L23: 0.4376 REMARK 3 S TENSOR REMARK 3 S11: -0.0331 S12: -0.4860 S13: 0.2574 REMARK 3 S21: -0.0262 S22: 0.3492 S23: 0.0370 REMARK 3 S31: 0.4771 S32: 0.4265 S33: -0.1946 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 278 THROUGH 327 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.8971 -32.6537 4.3309 REMARK 3 T TENSOR REMARK 3 T11: 0.9667 T22: 1.1605 REMARK 3 T33: 1.1602 T12: -0.0449 REMARK 3 T13: -0.0392 T23: -0.0181 REMARK 3 L TENSOR REMARK 3 L11: 2.2003 L22: 1.7172 REMARK 3 L33: 5.0273 L12: -0.4645 REMARK 3 L13: -2.5229 L23: 1.4498 REMARK 3 S TENSOR REMARK 3 S11: 0.2560 S12: 1.0061 S13: -0.4067 REMARK 3 S21: -0.5901 S22: -0.0254 S23: 0.0636 REMARK 3 S31: 0.4572 S32: 0.2207 S33: -0.0612 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 328 THROUGH 349 ) REMARK 3 ORIGIN FOR THE GROUP (A): -47.8226 -39.2550 -2.1470 REMARK 3 T TENSOR REMARK 3 T11: 0.6313 T22: 1.9078 REMARK 3 T33: 1.7032 T12: -0.4137 REMARK 3 T13: 0.2088 T23: -0.3246 REMARK 3 L TENSOR REMARK 3 L11: 0.0299 L22: 4.7500 REMARK 3 L33: 5.9964 L12: -0.1682 REMARK 3 L13: 0.1429 L23: -5.3090 REMARK 3 S TENSOR REMARK 3 S11: -0.5975 S12: 0.8925 S13: 1.7826 REMARK 3 S21: -0.9019 S22: -0.6027 S23: 1.8072 REMARK 3 S31: 1.2065 S32: -1.2858 S33: -0.2134 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 350 THROUGH 391 ) REMARK 3 ORIGIN FOR THE GROUP (A): -31.0234 -37.1612 8.0101 REMARK 3 T TENSOR REMARK 3 T11: 0.9591 T22: 0.9848 REMARK 3 T33: 0.9926 T12: -0.0061 REMARK 3 T13: -0.0985 T23: -0.1525 REMARK 3 L TENSOR REMARK 3 L11: 4.0271 L22: 3.5857 REMARK 3 L33: 3.3106 L12: -0.7749 REMARK 3 L13: 1.5610 L23: 0.0756 REMARK 3 S TENSOR REMARK 3 S11: -0.3030 S12: 0.4703 S13: -0.9449 REMARK 3 S21: -0.3902 S22: 0.0035 S23: 0.4029 REMARK 3 S31: 1.4511 S32: -1.7480 S33: 0.2372 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 392 THROUGH 442 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.9881 -30.3942 13.4147 REMARK 3 T TENSOR REMARK 3 T11: 0.6304 T22: 0.7172 REMARK 3 T33: 0.9634 T12: 0.0320 REMARK 3 T13: -0.0980 T23: 0.0502 REMARK 3 L TENSOR REMARK 3 L11: 2.1572 L22: 1.3074 REMARK 3 L33: 4.0255 L12: -1.2735 REMARK 3 L13: -0.8851 L23: 1.8981 REMARK 3 S TENSOR REMARK 3 S11: 0.0728 S12: 0.4093 S13: -0.4868 REMARK 3 S21: -0.2588 S22: -0.0251 S23: 0.2131 REMARK 3 S31: 0.0768 S32: 0.0721 S33: -0.1280 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 7R4J 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_1292120907. 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20060 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.950 REMARK 200 RESOLUTION RANGE LOW (A) : 48.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 200 DATA REDUNDANCY : 2.690 REMARK 200 R MERGE (I) : 0.12100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 2.03900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.460 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 (%): 57.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.91 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 110.80750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.23600 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.23600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 166.21125 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.23600 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.23600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 55.40375 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.23600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.23600 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 166.21125 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.23600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.23600 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 55.40375 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 110.80750 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: 3840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 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 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 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 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 GLN A 341 REMARK 465 GLY A 342 REMARK 465 ASN A 343 REMARK 465 LEU A 344 REMARK 465 ASN A 383 REMARK 465 ARG A 384 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 LEU A 100 CG CD1 CD2 REMARK 470 LEU A 101 CG CD1 CD2 REMARK 470 LEU A 103 CG CD1 CD2 REMARK 470 LYS A 104 CG CD CE NZ REMARK 470 ARG A 187 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 329 CG CD OE1 NE2 REMARK 470 ARG A 340 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 346 CG CD1 CD2 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 2.15 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 ARG A 142 NE2 GLN A 442 6545 1.97 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 66 109.73 -166.36 REMARK 500 LEU A 101 -116.10 66.85 REMARK 500 ALA A 102 -71.47 61.26 REMARK 500 LEU A 103 -118.95 74.59 REMARK 500 SER A 106 32.57 -88.25 REMARK 500 TYR A 108 -48.03 59.60 REMARK 500 ARG A 174 5.27 -64.50 REMARK 500 ASN A 182 92.43 -65.17 REMARK 500 ASP A 184 87.13 -160.93 REMARK 500 ARG A 187 -32.13 -132.76 REMARK 500 HIS A 191 8.25 -67.87 REMARK 500 SER A 201 62.72 -118.26 REMARK 500 HIS A 239 10.29 -61.20 REMARK 500 ASN A 276 -65.19 -92.18 REMARK 500 ALA A 318 -111.30 -93.80 REMARK 500 ALA A 338 25.48 -79.14 REMARK 500 LEU A 348 87.17 67.79 REMARK 500 SER A 388 -101.32 -121.82 REMARK 500 SER A 389 -173.09 58.85 REMARK 500 ARG A 390 83.94 32.77 REMARK 500 PHE A 419 61.16 -152.89 REMARK 500 GLU A 432 0.94 -63.43 REMARK 500 LEU A 440 -158.17 -125.99 REMARK 500 REMARK 500 REMARK: NULL DBREF 7R4J A 61 442 UNP Q4G0N4 NAKD2_HUMAN 61 442 SEQADV 7R4J MET A 52 UNP Q4G0N4 INITIATING METHIONINE SEQADV 7R4J GLY A 53 UNP Q4G0N4 EXPRESSION TAG SEQADV 7R4J HIS A 54 UNP Q4G0N4 EXPRESSION TAG SEQADV 7R4J HIS A 55 UNP Q4G0N4 EXPRESSION TAG SEQADV 7R4J HIS A 56 UNP Q4G0N4 EXPRESSION TAG SEQADV 7R4J HIS A 57 UNP Q4G0N4 EXPRESSION TAG SEQADV 7R4J HIS A 58 UNP Q4G0N4 EXPRESSION TAG SEQADV 7R4J HIS A 59 UNP Q4G0N4 EXPRESSION TAG SEQADV 7R4J 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 CA A 501 1 HET CA A 502 1 HETNAM CA CALCIUM ION FORMUL 2 CA 2(CA 2+) FORMUL 4 HOH *21(H2 O) HELIX 1 AA1 THR A 78 TYR A 87 1 10 HELIX 2 AA2 GLY A 110 ASN A 131 1 22 HELIX 3 AA3 ARG A 142 TYR A 144 5 3 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 SER A 201 1 7 HELIX 7 AA7 SER A 201 GLY A 212 1 12 HELIX 8 AA8 GLY A 313 LYS A 317 5 5 HELIX 9 AA9 ALA A 318 ARG A 325 1 8 HELIX 10 AB1 VAL A 331 ALA A 338 1 8 HELIX 11 AB2 ASN A 349 ASN A 361 1 13 HELIX 12 AB3 LYS A 431 GLU A 434 5 4 SHEET 1 AA1 5 GLU A 135 LYS A 140 0 SHEET 2 AA1 5 ARG A 70 ALA A 75 1 N VAL A 73 O VAL A 139 SHEET 3 AA1 5 ALA A 154 GLY A 159 1 O ILE A 156 N VAL A 72 SHEET 4 AA1 5 VAL A 178 ASN A 182 1 O VAL A 181 N ALA A 157 SHEET 5 AA1 5 CYS A 193 LEU A 194 1 O LEU A 194 N GLY A 180 SHEET 1 AA2 2 ARG A 215 ARG A 219 0 SHEET 2 AA2 2 LEU A 435 LEU A 439 -1 O LEU A 435 N ARG A 219 SHEET 1 AA3 6 SER A 265 ALA A 274 0 SHEET 2 AA3 6 ILE A 222 GLY A 228 -1 N ILE A 222 O ALA A 274 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 VAL A 398 O MET A 427 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 4 VAL A 236 ASP A 237 0 SHEET 2 AA4 4 THR A 415 GLU A 418 -1 O SER A 416 N VAL A 236 SHEET 3 AA4 4 ALA A 407 VAL A 411 -1 N VAL A 411 O THR A 415 SHEET 4 AA4 4 VAL A 278 GLU A 282 -1 N PHE A 279 O VAL A 410 SHEET 1 AA5 3 LEU A 308 CYS A 311 0 SHEET 2 AA5 3 ILE A 373 ILE A 377 -1 O SER A 376 N ASN A 309 SHEET 3 AA5 3 ARG A 392 SER A 395 -1 O SER A 395 N ILE A 373 LINK OD2 ASP A 127 CA CA A 501 1555 1555 2.60 LINK O GLY A 230 CA CA A 502 1555 1555 2.41 CRYST1 68.472 68.472 221.615 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 0.014605 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014605 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004512 0.00000 CONECT 437 2692 CONECT 1273 2693 CONECT 2692 437 CONECT 2693 1273 MASTER 486 0 2 12 20 0 0 6 2713 1 4 31 END