HEADER OXIDOREDUCTASE 02-JUL-26 43IA TITLE CRYSTAL STRUCTURE OF D-APIONATE OXIDOISOMERASE FROM AUREIMONAS TITLE 2 ALTAMIRENSIS IN COMPLEX WITH NAD+(H), ZN2+,AND MALONATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NADP OXIDOREDUCTASE COENZYME F420-DEPENDENT; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AUREIMONAS ALTAMIRENSIS; SOURCE 3 ORGANISM_TAXID: 370622; SOURCE 4 GENE: SAMN02745911_3050; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI DH5[ALPHA]; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 668369 KEYWDS D-APIOSE METABOLISM; D-APIONATE; OXIDOISOMERASE; METAL ENZYME, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.WATANABE,Y.AONO REVDAT 1 11-NOV-26 43IA 0 JRNL AUTH S.WATANABE,Y.AONO,S.I.TERAWAKI,H.SATO,T.YOKOI JRNL TITL STRUCTURAL BASIS FOR OXIDATION-COUPLED ISOMERIZATION BY JRNL TITL 2 APNO. JRNL REF J.BIOL.CHEM. 13628 2026 JRNL REFN ESSN 1083-351X JRNL PMID 42849729 JRNL DOI 10.1016/J.JBC.2026.113628 REMARK 2 REMARK 2 RESOLUTION. 1.26 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.26 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 151820 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 7727 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 46.5500 - 3.9100 1.00 5128 320 0.1526 0.1560 REMARK 3 2 3.9100 - 3.1100 1.00 4993 249 0.1533 0.1656 REMARK 3 3 3.1100 - 2.7100 1.00 4924 281 0.1791 0.1804 REMARK 3 4 2.7100 - 2.4700 1.00 4897 271 0.1781 0.1889 REMARK 3 5 2.4700 - 2.2900 1.00 4937 233 0.1648 0.1669 REMARK 3 6 2.2900 - 2.1500 1.00 4883 245 0.1569 0.1740 REMARK 3 7 2.1500 - 2.0500 1.00 4862 221 0.1561 0.1724 REMARK 3 8 2.0500 - 1.9600 1.00 4879 253 0.1563 0.1861 REMARK 3 9 1.9600 - 1.8800 1.00 4850 252 0.1585 0.1750 REMARK 3 10 1.8800 - 1.8200 1.00 4837 269 0.1564 0.1877 REMARK 3 11 1.8200 - 1.7600 1.00 4812 250 0.1580 0.1742 REMARK 3 12 1.7600 - 1.7100 0.99 4820 270 0.1568 0.1550 REMARK 3 13 1.7100 - 1.6700 0.99 4773 288 0.1522 0.1849 REMARK 3 14 1.6700 - 1.6200 0.99 4746 273 0.1474 0.1799 REMARK 3 15 1.6200 - 1.5900 0.99 4799 274 0.1525 0.1796 REMARK 3 16 1.5900 - 1.5500 0.99 4733 269 0.1507 0.1710 REMARK 3 17 1.5500 - 1.5200 0.99 4813 235 0.1496 0.1789 REMARK 3 18 1.5200 - 1.4900 0.99 4777 260 0.1544 0.1703 REMARK 3 19 1.4900 - 1.4700 0.99 4772 240 0.1583 0.1949 REMARK 3 20 1.4700 - 1.4400 0.99 4763 250 0.1924 0.2085 REMARK 3 21 1.4400 - 1.4200 0.99 4721 264 0.2255 0.2325 REMARK 3 22 1.4200 - 1.4000 0.99 4774 235 0.2487 0.2799 REMARK 3 23 1.4000 - 1.3800 0.98 4695 261 0.2354 0.2641 REMARK 3 24 1.3800 - 1.3600 0.98 4743 256 0.2252 0.2427 REMARK 3 25 1.3600 - 1.3400 0.98 4716 256 0.2253 0.2443 REMARK 3 26 1.3400 - 1.3200 0.98 4710 228 0.2225 0.2092 REMARK 3 27 1.3200 - 1.3100 0.98 4681 274 0.2393 0.2584 REMARK 3 28 1.3100 - 1.2900 0.98 4706 260 0.2602 0.2818 REMARK 3 29 1.2900 - 1.2700 0.98 4689 247 0.2990 0.3233 REMARK 3 30 1.2700 - 1.2600 0.97 4660 243 0.3366 0.3282 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.138 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.698 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.12 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.38 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 : 0.013 4353 REMARK 3 ANGLE : 1.357 5925 REMARK 3 CHIRALITY : 0.090 669 REMARK 3 PLANARITY : 0.012 769 REMARK 3 DIHEDRAL : 12.885 1607 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 2 THROUGH 275) REMARK 3 ORIGIN FOR THE GROUP (A): 5.3604 0.2556 -15.9170 REMARK 3 T TENSOR REMARK 3 T11: 0.0676 T22: 0.0611 REMARK 3 T33: 0.0838 T12: -0.0016 REMARK 3 T13: -0.0002 T23: -0.0038 REMARK 3 L TENSOR REMARK 3 L11: 0.2819 L22: 0.1490 REMARK 3 L33: 0.7168 L12: 0.0711 REMARK 3 L13: -0.2175 L23: -0.1081 REMARK 3 S TENSOR REMARK 3 S11: -0.0078 S12: 0.0319 S13: -0.0016 REMARK 3 S21: -0.0141 S22: 0.0052 S23: -0.0060 REMARK 3 S31: 0.0199 S32: 0.0322 S33: 0.0037 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 2 THROUGH 275) REMARK 3 ORIGIN FOR THE GROUP (A): -5.5188 2.5170 15.5126 REMARK 3 T TENSOR REMARK 3 T11: 0.0758 T22: 0.0651 REMARK 3 T33: 0.0921 T12: 0.0010 REMARK 3 T13: 0.0016 T23: 0.0018 REMARK 3 L TENSOR REMARK 3 L11: 0.1965 L22: 0.1665 REMARK 3 L33: 0.5098 L12: -0.0103 REMARK 3 L13: -0.1001 L23: 0.0463 REMARK 3 S TENSOR REMARK 3 S11: 0.0058 S12: -0.0080 S13: 0.0136 REMARK 3 S21: 0.0135 S22: 0.0037 S23: 0.0117 REMARK 3 S31: -0.0021 S32: -0.0363 S33: -0.0077 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : ens_1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "A" and (resid 2 through 39 or REMARK 3 resid 41 through 52 or (resid 53 through REMARK 3 55 and (name N or name CA or name C or REMARK 3 name O or name CB )) or resid 56 through REMARK 3 59 or (resid 60 and (name N or name CA or REMARK 3 name C or name O or name CB )) or resid REMARK 3 61 through 72 or (resid 73 and (name N or REMARK 3 name CA or name C or name O or name CB )) REMARK 3 or resid 74 through 82 or (resid 83 and REMARK 3 (name N or name CA or name C or name O or REMARK 3 name CB )) or resid 84 through 125 or REMARK 3 (resid 126 and (name N or name CA or name REMARK 3 C or name O or name CB )) or resid 127 REMARK 3 through 147 or resid 149 through 155 or REMARK 3 (resid 156 and (name N or name CA or name REMARK 3 C or name O or name CB )) or resid 157 REMARK 3 through 198 or resid 200 through 222 or REMARK 3 resid 224 through 249 or (resid 250 and REMARK 3 (name N or name CA or name C or name O or REMARK 3 name CB )) or resid 251 or resid 253 REMARK 3 through 275 or resid 301 through 302)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "B" and (resid 2 through 39 or REMARK 3 resid 41 through 147 or resid 149 through REMARK 3 198 or resid 200 through 222 or resid 224 REMARK 3 through 251 or resid 253 through 264 or REMARK 3 (resid 265 and (name N or name CA or name REMARK 3 C or name O or name CB )) or resid 266 REMARK 3 through 275 or resid 301 through 302)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 43IA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-JUL-26. REMARK 100 THE DEPOSITION ID IS D_1300076440. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAY-26 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 : SPRING-8 REMARK 200 BEAMLINE : BL45XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 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 : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 151911 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.260 REMARK 200 RESOLUTION RANGE LOW (A) : 46.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 25.80 REMARK 200 R MERGE (I) : 0.19600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.26 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 24.90 REMARK 200 R MERGE FOR SHELL (I) : 3.71900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 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 (%): 46.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM MALONATE PH 7.0 20% REMARK 280 POLYETHYLENE GLYCOL 3,350, EVAPORATION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 35.69750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.30750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.91150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.30750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.69750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.91150 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 13630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -194.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 -10 REMARK 465 ARG A -9 REMARK 465 GLY A -8 REMARK 465 SER A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 GLY A 0 REMARK 465 SER A 1 REMARK 465 MET B -10 REMARK 465 ARG B -9 REMARK 465 GLY B -8 REMARK 465 SER B -7 REMARK 465 HIS B -6 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 HIS B -2 REMARK 465 HIS B -1 REMARK 465 GLY B 0 REMARK 465 SER B 1 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 GLU A 152 CG CD OE1 OE2 REMARK 470 GLU A 265 CG CD OE1 OE2 REMARK 470 GLU B 53 CG CD OE1 OE2 REMARK 470 GLU B 60 CG CD OE1 OE2 REMARK 470 LYS B 73 CG CD CE NZ REMARK 470 LYS B 83 CG CD CE NZ REMARK 470 MET B 126 CG SD CE REMARK 470 GLU B 152 CG CD OE1 OE2 REMARK 470 LEU B 156 CG CD1 CD2 REMARK 470 LYS B 250 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 VAL B 90 CB VAL B 90 CG2 -0.135 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 HIS A 116 153.58 72.70 REMARK 500 ALA A 137 -32.65 -148.34 REMARK 500 MET A 169 -102.62 -100.92 REMARK 500 VAL A 190 -69.86 -93.54 REMARK 500 HIS B 116 153.47 74.11 REMARK 500 ALA B 137 -32.08 -150.81 REMARK 500 MET B 169 -102.08 -100.74 REMARK 500 VAL B 190 -70.01 -94.95 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 ZN A 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 113 NE2 REMARK 620 2 GLU A 183 OE1 110.0 REMARK 620 3 HIS B 222 NE2 116.3 95.0 REMARK 620 4 MLA B 301 O3A 123.9 96.4 109.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 222 NE2 REMARK 620 2 MLA A 302 O3B 109.9 REMARK 620 3 HIS B 113 NE2 116.3 122.8 REMARK 620 4 GLU B 183 OE1 96.0 96.8 109.5 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 26JC RELATED DB: PDB DBREF1 43IA A 2 275 UNP A0ABY1INU2_9HYPH DBREF2 43IA A A0ABY1INU2 2 275 DBREF1 43IA B 2 275 UNP A0ABY1INU2_9HYPH DBREF2 43IA B A0ABY1INU2 2 275 SEQADV 43IA MET A -10 UNP A0ABY1INU INITIATING METHIONINE SEQADV 43IA ARG A -9 UNP A0ABY1INU EXPRESSION TAG SEQADV 43IA GLY A -8 UNP A0ABY1INU EXPRESSION TAG SEQADV 43IA SER A -7 UNP A0ABY1INU EXPRESSION TAG SEQADV 43IA HIS A -6 UNP A0ABY1INU EXPRESSION TAG SEQADV 43IA HIS A -5 UNP A0ABY1INU EXPRESSION TAG SEQADV 43IA HIS A -4 UNP A0ABY1INU EXPRESSION TAG SEQADV 43IA HIS A -3 UNP A0ABY1INU EXPRESSION TAG SEQADV 43IA HIS A -2 UNP A0ABY1INU EXPRESSION TAG SEQADV 43IA HIS A -1 UNP A0ABY1INU EXPRESSION TAG SEQADV 43IA GLY A 0 UNP A0ABY1INU EXPRESSION TAG SEQADV 43IA SER A 1 UNP A0ABY1INU EXPRESSION TAG SEQADV 43IA MET B -10 UNP A0ABY1INU INITIATING METHIONINE SEQADV 43IA ARG B -9 UNP A0ABY1INU EXPRESSION TAG SEQADV 43IA GLY B -8 UNP A0ABY1INU EXPRESSION TAG SEQADV 43IA SER B -7 UNP A0ABY1INU EXPRESSION TAG SEQADV 43IA HIS B -6 UNP A0ABY1INU EXPRESSION TAG SEQADV 43IA HIS B -5 UNP A0ABY1INU EXPRESSION TAG SEQADV 43IA HIS B -4 UNP A0ABY1INU EXPRESSION TAG SEQADV 43IA HIS B -3 UNP A0ABY1INU EXPRESSION TAG SEQADV 43IA HIS B -2 UNP A0ABY1INU EXPRESSION TAG SEQADV 43IA HIS B -1 UNP A0ABY1INU EXPRESSION TAG SEQADV 43IA GLY B 0 UNP A0ABY1INU EXPRESSION TAG SEQADV 43IA SER B 1 UNP A0ABY1INU EXPRESSION TAG SEQRES 1 A 286 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER THR SEQRES 2 A 286 SER ILE ALA LEU PHE GLY ALA GLY GLY LYS MET GLY TYR SEQRES 3 A 286 ARG LEU ALA SER ASN LEU LYS GLY SER ARG PHE ASP VAL SEQRES 4 A 286 ARG HIS VAL GLU PRO SER GLU ALA GLY ALA LYS ARG LEU SEQRES 5 A 286 LYS ASP GLY LEU GLY PHE ASP CYS VAL PRO ALA GLU ALA SEQRES 6 A 286 ALA LEU ASP GLY ALA GLU VAL VAL VAL LEU ALA VAL PRO SEQRES 7 A 286 ASP THR LEU ILE GLY LYS VAL ALA ASN GLY ILE GLU LYS SEQRES 8 A 286 SER LEU LYS PRO GLY THR ILE VAL VAL VAL LEU ASP ALA SEQRES 9 A 286 ALA ALA PRO PHE ALA GLY HIS LEU PRO ASN ARG PRO ASP SEQRES 10 A 286 LEU THR TYR PHE VAL THR HIS PRO CYS HIS PRO PRO ILE SEQRES 11 A 286 PHE ASN ASP GLU THR GLU MET ASP ALA LYS ARG ASP PHE SEQRES 12 A 286 PHE GLY GLY ILE ALA ALA LYS GLN HIS ILE THR SER ALA SEQRES 13 A 286 LEU MET GLN GLY PRO ASP GLU HIS TYR ALA LEU GLY GLU SEQRES 14 A 286 GLU VAL ALA LYS VAL ILE TRP ALA PRO VAL MET ARG SER SEQRES 15 A 286 HIS ARG VAL THR VAL GLU GLN MET ALA LEU LEU GLU PRO SEQRES 16 A 286 GLY LEU SER GLU THR VAL CYS ALA SER LEU LEU VAL ALA SEQRES 17 A 286 MET LYS GLU ALA MET ASP GLU VAL VAL ALA ARG GLY VAL SEQRES 18 A 286 PRO LYS GLU ALA ALA ARG ASP PHE LEU LEU GLY HIS MET SEQRES 19 A 286 ASN VAL LEU GLY SER VAL ILE PHE GLU GLU THR PRO GLY SEQRES 20 A 286 VAL PHE SER ASP ALA CYS ASN LYS ALA ILE GLU PHE GLY SEQRES 21 A 286 LYS PRO MET LEU MET ARG ASP ASP TRP LYS ARG VAL PHE SEQRES 22 A 286 GLU PRO GLU GLU LEU ALA ALA SER ILE ARG ARG ILE THR SEQRES 1 B 286 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER THR SEQRES 2 B 286 SER ILE ALA LEU PHE GLY ALA GLY GLY LYS MET GLY TYR SEQRES 3 B 286 ARG LEU ALA SER ASN LEU LYS GLY SER ARG PHE ASP VAL SEQRES 4 B 286 ARG HIS VAL GLU PRO SER GLU ALA GLY ALA LYS ARG LEU SEQRES 5 B 286 LYS ASP GLY LEU GLY PHE ASP CYS VAL PRO ALA GLU ALA SEQRES 6 B 286 ALA LEU ASP GLY ALA GLU VAL VAL VAL LEU ALA VAL PRO SEQRES 7 B 286 ASP THR LEU ILE GLY LYS VAL ALA ASN GLY ILE GLU LYS SEQRES 8 B 286 SER LEU LYS PRO GLY THR ILE VAL VAL VAL LEU ASP ALA SEQRES 9 B 286 ALA ALA PRO PHE ALA GLY HIS LEU PRO ASN ARG PRO ASP SEQRES 10 B 286 LEU THR TYR PHE VAL THR HIS PRO CYS HIS PRO PRO ILE SEQRES 11 B 286 PHE ASN ASP GLU THR GLU MET ASP ALA LYS ARG ASP PHE SEQRES 12 B 286 PHE GLY GLY ILE ALA ALA LYS GLN HIS ILE THR SER ALA SEQRES 13 B 286 LEU MET GLN GLY PRO ASP GLU HIS TYR ALA LEU GLY GLU SEQRES 14 B 286 GLU VAL ALA LYS VAL ILE TRP ALA PRO VAL MET ARG SER SEQRES 15 B 286 HIS ARG VAL THR VAL GLU GLN MET ALA LEU LEU GLU PRO SEQRES 16 B 286 GLY LEU SER GLU THR VAL CYS ALA SER LEU LEU VAL ALA SEQRES 17 B 286 MET LYS GLU ALA MET ASP GLU VAL VAL ALA ARG GLY VAL SEQRES 18 B 286 PRO LYS GLU ALA ALA ARG ASP PHE LEU LEU GLY HIS MET SEQRES 19 B 286 ASN VAL LEU GLY SER VAL ILE PHE GLU GLU THR PRO GLY SEQRES 20 B 286 VAL PHE SER ASP ALA CYS ASN LYS ALA ILE GLU PHE GLY SEQRES 21 B 286 LYS PRO MET LEU MET ARG ASP ASP TRP LYS ARG VAL PHE SEQRES 22 B 286 GLU PRO GLU GLU LEU ALA ALA SER ILE ARG ARG ILE THR HET NAD A 301 44 HET MLA A 302 7 HET ZN A 303 1 HET MLA B 301 7 HET NAD B 302 44 HET ZN B 303 1 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM MLA MALONIC ACID HETNAM ZN ZINC ION HETSYN MLA DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; HETSYN 2 MLA METHANEDICARBOXYLIC ACID FORMUL 3 NAD 2(C21 H27 N7 O14 P2) FORMUL 4 MLA 2(C3 H4 O4) FORMUL 5 ZN 2(ZN 2+) FORMUL 9 HOH *807(H2 O) HELIX 1 AA1 GLY A 11 LYS A 22 1 12 HELIX 2 AA2 SER A 34 GLY A 46 1 13 HELIX 3 AA3 PRO A 51 ASP A 57 1 7 HELIX 4 AA4 PRO A 67 THR A 69 5 3 HELIX 5 AA5 LEU A 70 GLU A 79 1 10 HELIX 6 AA6 LYS A 80 LEU A 82 5 3 HELIX 7 AA7 ALA A 93 ALA A 98 1 6 HELIX 8 AA8 GLU A 125 ARG A 130 1 6 HELIX 9 AA9 PRO A 150 GLU A 152 5 3 HELIX 10 AB1 HIS A 153 TRP A 165 1 13 HELIX 11 AB2 THR A 175 GLU A 183 1 9 HELIX 12 AB3 VAL A 190 ARG A 208 1 19 HELIX 13 AB4 PRO A 211 PHE A 231 1 21 HELIX 14 AB5 SER A 239 MET A 254 1 16 HELIX 15 AB6 ASP A 257 PHE A 262 5 6 HELIX 16 AB7 GLU A 263 THR A 275 1 13 HELIX 17 AB8 GLY B 11 LYS B 22 1 12 HELIX 18 AB9 SER B 34 GLY B 46 1 13 HELIX 19 AC1 PRO B 51 ASP B 57 1 7 HELIX 20 AC2 LEU B 70 GLU B 79 1 10 HELIX 21 AC3 LYS B 80 LEU B 82 5 3 HELIX 22 AC4 ALA B 93 ALA B 98 1 6 HELIX 23 AC5 GLU B 125 ARG B 130 1 6 HELIX 24 AC6 GLU B 152 TRP B 165 1 14 HELIX 25 AC7 THR B 175 GLU B 183 1 9 HELIX 26 AC8 VAL B 190 ARG B 208 1 19 HELIX 27 AC9 PRO B 211 PHE B 231 1 21 HELIX 28 AD1 SER B 239 MET B 254 1 16 HELIX 29 AD2 ASP B 257 PHE B 262 5 6 HELIX 30 AD3 GLU B 263 THR B 275 1 13 SHEET 1 AA1 7 ASP A 27 VAL A 31 0 SHEET 2 AA1 7 SER A 3 PHE A 7 1 N LEU A 6 O VAL A 31 SHEET 3 AA1 7 VAL A 61 LEU A 64 1 O VAL A 63 N PHE A 7 SHEET 4 AA1 7 ILE A 87 VAL A 90 1 O VAL A 89 N VAL A 62 SHEET 5 AA1 7 THR A 108 PRO A 114 1 O THR A 108 N VAL A 88 SHEET 6 AA1 7 GLN A 140 GLN A 148 -1 O ALA A 145 N VAL A 111 SHEET 7 AA1 7 VAL A 168 ARG A 173 1 O HIS A 172 N ILE A 142 SHEET 1 AA2 7 ASP B 27 VAL B 31 0 SHEET 2 AA2 7 SER B 3 PHE B 7 1 N ILE B 4 O ARG B 29 SHEET 3 AA2 7 VAL B 61 LEU B 64 1 O VAL B 63 N ALA B 5 SHEET 4 AA2 7 ILE B 87 VAL B 90 1 O VAL B 89 N VAL B 62 SHEET 5 AA2 7 THR B 108 PRO B 114 1 O THR B 108 N VAL B 88 SHEET 6 AA2 7 GLN B 140 GLN B 148 -1 O ALA B 145 N VAL B 111 SHEET 7 AA2 7 VAL B 168 ARG B 173 1 O HIS B 172 N ILE B 142 LINK NE2 HIS A 113 ZN ZN A 303 1555 1555 2.04 LINK OE1 GLU A 183 ZN ZN A 303 1555 1555 2.00 LINK NE2 HIS A 222 ZN ZN B 303 1555 1555 2.09 LINK O3B MLA A 302 ZN ZN B 303 1555 1555 1.93 LINK ZN ZN A 303 NE2 HIS B 222 1555 1555 2.07 LINK ZN ZN A 303 O3A MLA B 301 1555 1555 1.87 LINK NE2 HIS B 113 ZN ZN B 303 1555 1555 2.04 LINK OE1 GLU B 183 ZN ZN B 303 1555 1555 2.00 CISPEP 1 ALA A 166 PRO A 167 0 -0.17 CISPEP 2 GLU A 183 PRO A 184 0 17.75 CISPEP 3 ALA B 166 PRO B 167 0 0.61 CISPEP 4 GLU B 183 PRO B 184 0 16.07 CRYST1 71.395 75.823 104.615 90.00 90.00 90.00 P 21 21 21 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 0.014007 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013189 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009559 0.00000 MTRIX1 1 -0.996968 0.075330 -0.019525 -0.58140 1 MTRIX2 1 0.077205 0.988914 -0.126841 0.02602 1 MTRIX3 1 0.009753 -0.127964 -0.991731 0.02375 1 CONECT 827 4205 CONECT 1378 4205 CONECT 1664 4257 CONECT 2892 4257 CONECT 3431 4257 CONECT 3723 4205 CONECT 4154 4155 4156 4157 4176 CONECT 4155 4154 CONECT 4156 4154 CONECT 4157 4154 4158 CONECT 4158 4157 4159 CONECT 4159 4158 4160 4161 CONECT 4160 4159 4165 CONECT 4161 4159 4162 4163 CONECT 4162 4161 CONECT 4163 4161 4164 4165 CONECT 4164 4163 CONECT 4165 4160 4163 4166 CONECT 4166 4165 4167 4175 CONECT 4167 4166 4168 CONECT 4168 4167 4169 CONECT 4169 4168 4170 4175 CONECT 4170 4169 4171 4172 CONECT 4171 4170 CONECT 4172 4170 4173 CONECT 4173 4172 4174 CONECT 4174 4173 4175 CONECT 4175 4166 4169 4174 CONECT 4176 4154 4177 CONECT 4177 4176 4178 4179 4180 CONECT 4178 4177 CONECT 4179 4177 CONECT 4180 4177 4181 CONECT 4181 4180 4182 CONECT 4182 4181 4183 4184 CONECT 4183 4182 4188 CONECT 4184 4182 4185 4186 CONECT 4185 4184 CONECT 4186 4184 4187 4188 CONECT 4187 4186 CONECT 4188 4183 4186 4189 CONECT 4189 4188 4190 4197 CONECT 4190 4189 4191 CONECT 4191 4190 4192 4195 CONECT 4192 4191 4193 4194 CONECT 4193 4192 CONECT 4194 4192 CONECT 4195 4191 4196 CONECT 4196 4195 4197 CONECT 4197 4189 4196 CONECT 4198 4199 4200 4201 CONECT 4199 4198 CONECT 4200 4198 CONECT 4201 4198 4202 CONECT 4202 4201 4203 4204 CONECT 4203 4202 CONECT 4204 4202 4257 CONECT 4205 827 1378 3723 4211 CONECT 4206 4207 4208 4209 CONECT 4207 4206 CONECT 4208 4206 CONECT 4209 4206 4210 CONECT 4210 4209 4211 4212 CONECT 4211 4205 4210 CONECT 4212 4210 CONECT 4213 4214 4215 4216 4235 CONECT 4214 4213 CONECT 4215 4213 CONECT 4216 4213 4217 CONECT 4217 4216 4218 CONECT 4218 4217 4219 4220 CONECT 4219 4218 4224 CONECT 4220 4218 4221 4222 CONECT 4221 4220 CONECT 4222 4220 4223 4224 CONECT 4223 4222 CONECT 4224 4219 4222 4225 CONECT 4225 4224 4226 4234 CONECT 4226 4225 4227 CONECT 4227 4226 4228 CONECT 4228 4227 4229 4234 CONECT 4229 4228 4230 4231 CONECT 4230 4229 CONECT 4231 4229 4232 CONECT 4232 4231 4233 CONECT 4233 4232 4234 CONECT 4234 4225 4228 4233 CONECT 4235 4213 4236 CONECT 4236 4235 4237 4238 4239 CONECT 4237 4236 CONECT 4238 4236 CONECT 4239 4236 4240 CONECT 4240 4239 4241 CONECT 4241 4240 4242 4243 CONECT 4242 4241 4247 CONECT 4243 4241 4244 4245 CONECT 4244 4243 CONECT 4245 4243 4246 4247 CONECT 4246 4245 CONECT 4247 4242 4245 4248 CONECT 4248 4247 4249 4256 CONECT 4249 4248 4250 CONECT 4250 4249 4251 4254 CONECT 4251 4250 4252 4253 CONECT 4252 4251 CONECT 4253 4251 CONECT 4254 4250 4255 CONECT 4255 4254 4256 CONECT 4256 4248 4255 CONECT 4257 1664 2892 3431 4204 MASTER 404 0 6 30 14 0 0 9 5027 2 110 44 END