HEADER BIOSYNTHETIC PROTEIN 10-JAN-23 8HZY TITLE THE CRYSTAL STRUCTURE OF A RADICAL SAM ENZYME DESII COMPND MOL_ID: 1; COMPND 2 MOLECULE: DESII; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RADICAL S-ADENOSYL-L-METHIONINE ENZYME, DEAMINATION, DEHYDROGENASE, KEYWDS 2 BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.L.HOU,J.H.ZHOU REVDAT 1 10-JUL-24 8HZY 0 JRNL AUTH X.HOU,J.FENG,J.L.FRANKLIN,R.RUSSO,Z.GUO,J.ZHOU,J.M.GAO, JRNL AUTH 2 H.W.LIU,B.WANG JRNL TITL MECHANISTIC INSIGHTS FROM THE CRYSTAL STRUCTURE AND JRNL TITL 2 COMPUTATIONAL ANALYSIS OF THE RADICAL SAM DEAMINASE DESII. JRNL REF ADV SCI 03494 2024 JRNL REFN ESSN 2198-3844 JRNL PMID 38943270 JRNL DOI 10.1002/ADVS.202403494 REMARK 2 REMARK 2 RESOLUTION. 2.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.453 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 77578 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.043 REMARK 3 FREE R VALUE TEST SET COUNT : 3912 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 32.9780 - 6.1809 0.99 2812 147 0.1853 0.1781 REMARK 3 2 6.1809 - 4.9111 1.00 2721 137 0.2087 0.2195 REMARK 3 3 4.9111 - 4.2919 1.00 2697 150 0.1659 0.2172 REMARK 3 4 4.2919 - 3.9001 1.00 2668 134 0.1684 0.1841 REMARK 3 5 3.9001 - 3.6210 1.00 2650 148 0.1784 0.2015 REMARK 3 6 3.6210 - 3.4077 1.00 2632 148 0.1840 0.2348 REMARK 3 7 3.4077 - 3.2372 1.00 2640 157 0.1901 0.2594 REMARK 3 8 3.2372 - 3.0964 1.00 2624 131 0.1999 0.2199 REMARK 3 9 3.0964 - 2.9773 1.00 2657 134 0.2082 0.2699 REMARK 3 10 2.9773 - 2.8746 1.00 2619 143 0.2029 0.2489 REMARK 3 11 2.8746 - 2.7848 1.00 2599 159 0.2062 0.2770 REMARK 3 12 2.7848 - 2.7052 1.00 2634 133 0.2116 0.2590 REMARK 3 13 2.7052 - 2.6340 1.00 2621 118 0.2190 0.3002 REMARK 3 14 2.6340 - 2.5698 1.00 2658 118 0.2041 0.2676 REMARK 3 15 2.5698 - 2.5114 1.00 2595 134 0.2106 0.2542 REMARK 3 16 2.5114 - 2.4579 1.00 2650 134 0.2160 0.2469 REMARK 3 17 2.4579 - 2.4088 1.00 2623 133 0.2178 0.2520 REMARK 3 18 2.4088 - 2.3633 1.00 2582 121 0.2216 0.2360 REMARK 3 19 2.3633 - 2.3212 1.00 2602 138 0.2237 0.2613 REMARK 3 20 2.3212 - 2.2818 1.00 2658 134 0.2202 0.2958 REMARK 3 21 2.2818 - 2.2450 1.00 2570 149 0.2290 0.2650 REMARK 3 22 2.2450 - 2.2105 1.00 2578 153 0.2346 0.2956 REMARK 3 23 2.2105 - 2.1780 1.00 2619 141 0.2404 0.3021 REMARK 3 24 2.1780 - 2.1473 1.00 2596 140 0.2493 0.3118 REMARK 3 25 2.1473 - 2.1183 1.00 2602 142 0.2550 0.2617 REMARK 3 26 2.1183 - 2.0908 1.00 2591 149 0.2591 0.2795 REMARK 3 27 2.0908 - 2.0647 1.00 2575 125 0.2695 0.3241 REMARK 3 28 2.0647 - 2.0398 0.99 2593 162 0.2824 0.3132 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) : 0.233 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.736 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.01 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 : 0.005 7324 REMARK 3 ANGLE : 0.771 9966 REMARK 3 CHIRALITY : 0.047 1078 REMARK 3 PLANARITY : 0.005 1340 REMARK 3 DIHEDRAL : 14.700 4365 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 23.6344 -63.9106 -10.6900 REMARK 3 T TENSOR REMARK 3 T11: 0.0765 T22: 0.1023 REMARK 3 T33: 0.0958 T12: -0.0168 REMARK 3 T13: 0.0065 T23: 0.0027 REMARK 3 L TENSOR REMARK 3 L11: 0.0790 L22: 0.2939 REMARK 3 L33: 0.0984 L12: -0.1370 REMARK 3 L13: 0.0121 L23: -0.0310 REMARK 3 S TENSOR REMARK 3 S11: -0.0044 S12: 0.0033 S13: -0.0198 REMARK 3 S21: 0.0051 S22: 0.0042 S23: 0.0171 REMARK 3 S31: 0.0263 S32: -0.0151 S33: 0.0015 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 8HZY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1300034681. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAR-22 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 : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785 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 : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 77686 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.030 REMARK 200 RESOLUTION RANGE LOW (A) : 32.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.08 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 : 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES MONOHYDRATE PH 6.0, 20% PEG REMARK 280 6000 AND 1.0 M LICL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,-Y,-Z+1/2 REMARK 290 4555 -X+1/2,-Y,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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 48.54400 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.12400 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 48.54400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 59.12400 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 715 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 HIS A -24 REMARK 465 HIS A -23 REMARK 465 HIS A -22 REMARK 465 HIS A -21 REMARK 465 HIS A -20 REMARK 465 HIS A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 GLY A -16 REMARK 465 SER A -15 REMARK 465 ASP A -14 REMARK 465 TYR A -13 REMARK 465 ASP A -12 REMARK 465 ILE A -11 REMARK 465 PRO A -10 REMARK 465 THR A -9 REMARK 465 THR A -8 REMARK 465 GLU A -7 REMARK 465 ASN A -6 REMARK 465 LEU A -5 REMARK 465 TYR A -4 REMARK 465 PHE A -3 REMARK 465 GLN A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 ALA A 3 REMARK 465 PRO A 4 REMARK 465 ALA A 5 REMARK 465 LEU A 6 REMARK 465 SER A 7 REMARK 465 ALA A 8 REMARK 465 THR A 9 REMARK 465 TYR A 324 REMARK 465 SER A 325 REMARK 465 GLY A 326 REMARK 465 ARG A 327 REMARK 465 ASP A 328 REMARK 465 ASP A 329 REMARK 465 GLY A 330 REMARK 465 LYS A 331 REMARK 465 LEU A 332 REMARK 465 PRO A 333 REMARK 465 GLN A 334 REMARK 465 GLU A 335 REMARK 465 GLU A 336 REMARK 465 ARG A 337 REMARK 465 HIS B -24 REMARK 465 HIS B -23 REMARK 465 HIS B -22 REMARK 465 HIS B -21 REMARK 465 HIS B -20 REMARK 465 HIS B -19 REMARK 465 HIS B -18 REMARK 465 HIS B -17 REMARK 465 GLY B -16 REMARK 465 SER B -15 REMARK 465 ASP B -14 REMARK 465 TYR B -13 REMARK 465 ASP B -12 REMARK 465 ILE B -11 REMARK 465 PRO B -10 REMARK 465 THR B -9 REMARK 465 THR B -8 REMARK 465 GLU B -7 REMARK 465 ASN B -6 REMARK 465 LEU B -5 REMARK 465 TYR B -4 REMARK 465 PHE B -3 REMARK 465 GLN B -2 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 ALA B 3 REMARK 465 PRO B 4 REMARK 465 ALA B 5 REMARK 465 LEU B 6 REMARK 465 SER B 7 REMARK 465 ALA B 8 REMARK 465 THR B 9 REMARK 465 ASP B 323 REMARK 465 TYR B 324 REMARK 465 SER B 325 REMARK 465 GLY B 326 REMARK 465 ARG B 327 REMARK 465 ASP B 328 REMARK 465 ASP B 329 REMARK 465 GLY B 330 REMARK 465 LYS B 331 REMARK 465 LEU B 332 REMARK 465 PRO B 333 REMARK 465 GLN B 334 REMARK 465 GLU B 335 REMARK 465 GLU B 336 REMARK 465 ASP B 374 REMARK 465 ALA B 375 REMARK 465 GLU B 376 REMARK 465 LEU B 377 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 NH1 ARG B 169 O HOH B 601 1.98 REMARK 500 OE2 GLU B 190 N MET B 501 2.17 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 ASP A 76 151.37 -46.25 REMARK 500 THR A 109 -60.00 -134.64 REMARK 500 ARG A 144 51.51 -142.33 REMARK 500 VAL A 151 37.87 -77.48 REMARK 500 SER A 186 -151.32 -152.47 REMARK 500 SER A 217 12.97 58.34 REMARK 500 ALA A 389 -151.34 54.72 REMARK 500 TRP A 477 57.06 -114.10 REMARK 500 PHE A 483 -62.69 70.14 REMARK 500 THR B 109 -56.33 -126.70 REMARK 500 SER B 186 -153.21 -156.35 REMARK 500 SER B 217 17.54 58.47 REMARK 500 ALA B 338 26.17 -75.90 REMARK 500 ALA B 389 -151.45 49.52 REMARK 500 TRP B 477 55.30 -113.50 REMARK 500 PHE B 483 -64.78 67.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 187 GLY A 188 125.58 REMARK 500 GLY B 187 GLY B 188 125.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 909 DISTANCE = 6.34 ANGSTROMS 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 SF4 A 501 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 141 SG REMARK 620 2 SF4 A 501 S2 113.7 REMARK 620 3 SF4 A 501 S3 101.0 104.3 REMARK 620 4 SF4 A 501 S4 126.0 103.9 105.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 501 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 145 SG REMARK 620 2 SF4 A 501 S1 111.2 REMARK 620 3 SF4 A 501 S3 118.5 103.9 REMARK 620 4 SF4 A 501 S4 112.6 103.7 105.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 501 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 625 O REMARK 620 2 SF4 A 501 S1 73.1 REMARK 620 3 SF4 A 501 S2 157.6 102.7 REMARK 620 4 SF4 A 501 S3 99.3 104.7 103.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 502 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 141 SG REMARK 620 2 SF4 B 502 S1 98.6 REMARK 620 3 SF4 B 502 S2 109.8 106.3 REMARK 620 4 SF4 B 502 S3 130.2 105.3 104.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 502 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 145 SG REMARK 620 2 SF4 B 502 S1 114.8 REMARK 620 3 SF4 B 502 S3 102.7 104.3 REMARK 620 4 SF4 B 502 S4 123.6 104.8 104.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 502 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 148 SG REMARK 620 2 SF4 B 502 S2 119.1 REMARK 620 3 SF4 B 502 S3 108.8 104.9 REMARK 620 4 SF4 B 502 S4 115.3 102.7 104.6 REMARK 620 N 1 2 3 DBREF 8HZY A -24 485 PDB 8HZY 8HZY -24 485 DBREF 8HZY B -24 485 PDB 8HZY 8HZY -24 485 SEQRES 1 A 510 HIS HIS HIS HIS HIS HIS HIS HIS GLY SER ASP TYR ASP SEQRES 2 A 510 ILE PRO THR THR GLU ASN LEU TYR PHE GLN GLY SER MET SEQRES 3 A 510 THR ALA PRO ALA LEU SER ALA THR ALA PRO ALA GLU ARG SEQRES 4 A 510 CYS ALA HIS PRO GLY ALA ASP LEU GLY ALA ALA VAL HIS SEQRES 5 A 510 ALA VAL GLY GLN THR LEU ALA ALA GLY GLY LEU VAL PRO SEQRES 6 A 510 PRO ASP GLU ALA GLY THR THR ALA ARG HIS LEU VAL ARG SEQRES 7 A 510 LEU ALA VAL ARG TYR GLY ASN SER PRO PHE THR PRO LEU SEQRES 8 A 510 GLU GLU ALA ARG HIS ASP LEU GLY VAL ASP ARG ASP ALA SEQRES 9 A 510 PHE ARG ARG LEU LEU ALA LEU PHE GLY GLN VAL PRO GLU SEQRES 10 A 510 LEU ARG THR ALA VAL GLU THR GLY PRO ALA GLY ALA TYR SEQRES 11 A 510 TRP LYS ASN THR LEU LEU PRO LEU GLU GLN ARG GLY VAL SEQRES 12 A 510 PHE ASP ALA ALA LEU ALA ARG LYS PRO VAL PHE PRO TYR SEQRES 13 A 510 SER VAL GLY LEU TYR PRO GLY PRO THR CYS MET PHE ARG SEQRES 14 A 510 CYS HIS PHE CYS VAL ARG VAL THR GLY ALA ARG TYR ASP SEQRES 15 A 510 PRO SER ALA LEU ASP ALA GLY ASN ALA MET PHE ARG SER SEQRES 16 A 510 VAL ILE ASP GLU ILE PRO ALA GLY ASN PRO SER ALA MET SEQRES 17 A 510 TYR PHE SER GLY GLY LEU GLU PRO LEU THR ASN PRO GLY SEQRES 18 A 510 LEU GLY SER LEU ALA ALA HIS ALA THR ASP HIS GLY LEU SEQRES 19 A 510 ARG PRO THR VAL TYR THR ASN SER PHE ALA LEU THR GLU SEQRES 20 A 510 ARG THR LEU GLU ARG GLN PRO GLY LEU TRP GLY LEU HIS SEQRES 21 A 510 ALA ILE ARG THR SER LEU TYR GLY LEU ASN ASP GLU GLU SEQRES 22 A 510 TYR GLU GLN THR THR GLY LYS LYS ALA ALA PHE ARG ARG SEQRES 23 A 510 VAL ARG GLU ASN LEU ARG ARG PHE GLN GLN LEU ARG ALA SEQRES 24 A 510 GLU ARG GLU SER PRO ILE ASN LEU GLY PHE ALA TYR ILE SEQRES 25 A 510 VAL LEU PRO GLY ARG ALA SER ARG LEU LEU ASP LEU VAL SEQRES 26 A 510 ASP PHE ILE ALA ASP LEU ASN ASP ALA GLY GLN GLY ARG SEQRES 27 A 510 THR ILE ASP PHE VAL ASN ILE ARG GLU ASP TYR SER GLY SEQRES 28 A 510 ARG ASP ASP GLY LYS LEU PRO GLN GLU GLU ARG ALA GLU SEQRES 29 A 510 LEU GLN GLU ALA LEU ASN ALA PHE GLU GLU ARG VAL ARG SEQRES 30 A 510 GLU ARG THR PRO GLY LEU HIS ILE ASP TYR GLY TYR ALA SEQRES 31 A 510 LEU ASN SER LEU ARG THR GLY ALA ASP ALA GLU LEU LEU SEQRES 32 A 510 ARG ILE LYS PRO ALA THR MET ARG PRO THR ALA HIS PRO SEQRES 33 A 510 GLN VAL ALA VAL GLN VAL ASP LEU LEU GLY ASP VAL TYR SEQRES 34 A 510 LEU TYR ARG GLU ALA GLY PHE PRO ASP LEU ASP GLY ALA SEQRES 35 A 510 THR ARG TYR ILE ALA GLY ARG VAL THR PRO ASP THR SER SEQRES 36 A 510 LEU THR GLU VAL VAL ARG ASP PHE VAL GLU ARG GLY GLY SEQRES 37 A 510 GLU VAL ALA ALA VAL ASP GLY ASP GLU TYR PHE MET ASP SEQRES 38 A 510 GLY PHE ASP GLN VAL VAL THR ALA ARG LEU ASN GLN LEU SEQRES 39 A 510 GLU ARG ASP ALA ALA ASP GLY TRP GLU GLU ALA ARG GLY SEQRES 40 A 510 PHE LEU ARG SEQRES 1 B 510 HIS HIS HIS HIS HIS HIS HIS HIS GLY SER ASP TYR ASP SEQRES 2 B 510 ILE PRO THR THR GLU ASN LEU TYR PHE GLN GLY SER MET SEQRES 3 B 510 THR ALA PRO ALA LEU SER ALA THR ALA PRO ALA GLU ARG SEQRES 4 B 510 CYS ALA HIS PRO GLY ALA ASP LEU GLY ALA ALA VAL HIS SEQRES 5 B 510 ALA VAL GLY GLN THR LEU ALA ALA GLY GLY LEU VAL PRO SEQRES 6 B 510 PRO ASP GLU ALA GLY THR THR ALA ARG HIS LEU VAL ARG SEQRES 7 B 510 LEU ALA VAL ARG TYR GLY ASN SER PRO PHE THR PRO LEU SEQRES 8 B 510 GLU GLU ALA ARG HIS ASP LEU GLY VAL ASP ARG ASP ALA SEQRES 9 B 510 PHE ARG ARG LEU LEU ALA LEU PHE GLY GLN VAL PRO GLU SEQRES 10 B 510 LEU ARG THR ALA VAL GLU THR GLY PRO ALA GLY ALA TYR SEQRES 11 B 510 TRP LYS ASN THR LEU LEU PRO LEU GLU GLN ARG GLY VAL SEQRES 12 B 510 PHE ASP ALA ALA LEU ALA ARG LYS PRO VAL PHE PRO TYR SEQRES 13 B 510 SER VAL GLY LEU TYR PRO GLY PRO THR CYS MET PHE ARG SEQRES 14 B 510 CYS HIS PHE CYS VAL ARG VAL THR GLY ALA ARG TYR ASP SEQRES 15 B 510 PRO SER ALA LEU ASP ALA GLY ASN ALA MET PHE ARG SER SEQRES 16 B 510 VAL ILE ASP GLU ILE PRO ALA GLY ASN PRO SER ALA MET SEQRES 17 B 510 TYR PHE SER GLY GLY LEU GLU PRO LEU THR ASN PRO GLY SEQRES 18 B 510 LEU GLY SER LEU ALA ALA HIS ALA THR ASP HIS GLY LEU SEQRES 19 B 510 ARG PRO THR VAL TYR THR ASN SER PHE ALA LEU THR GLU SEQRES 20 B 510 ARG THR LEU GLU ARG GLN PRO GLY LEU TRP GLY LEU HIS SEQRES 21 B 510 ALA ILE ARG THR SER LEU TYR GLY LEU ASN ASP GLU GLU SEQRES 22 B 510 TYR GLU GLN THR THR GLY LYS LYS ALA ALA PHE ARG ARG SEQRES 23 B 510 VAL ARG GLU ASN LEU ARG ARG PHE GLN GLN LEU ARG ALA SEQRES 24 B 510 GLU ARG GLU SER PRO ILE ASN LEU GLY PHE ALA TYR ILE SEQRES 25 B 510 VAL LEU PRO GLY ARG ALA SER ARG LEU LEU ASP LEU VAL SEQRES 26 B 510 ASP PHE ILE ALA ASP LEU ASN ASP ALA GLY GLN GLY ARG SEQRES 27 B 510 THR ILE ASP PHE VAL ASN ILE ARG GLU ASP TYR SER GLY SEQRES 28 B 510 ARG ASP ASP GLY LYS LEU PRO GLN GLU GLU ARG ALA GLU SEQRES 29 B 510 LEU GLN GLU ALA LEU ASN ALA PHE GLU GLU ARG VAL ARG SEQRES 30 B 510 GLU ARG THR PRO GLY LEU HIS ILE ASP TYR GLY TYR ALA SEQRES 31 B 510 LEU ASN SER LEU ARG THR GLY ALA ASP ALA GLU LEU LEU SEQRES 32 B 510 ARG ILE LYS PRO ALA THR MET ARG PRO THR ALA HIS PRO SEQRES 33 B 510 GLN VAL ALA VAL GLN VAL ASP LEU LEU GLY ASP VAL TYR SEQRES 34 B 510 LEU TYR ARG GLU ALA GLY PHE PRO ASP LEU ASP GLY ALA SEQRES 35 B 510 THR ARG TYR ILE ALA GLY ARG VAL THR PRO ASP THR SER SEQRES 36 B 510 LEU THR GLU VAL VAL ARG ASP PHE VAL GLU ARG GLY GLY SEQRES 37 B 510 GLU VAL ALA ALA VAL ASP GLY ASP GLU TYR PHE MET ASP SEQRES 38 B 510 GLY PHE ASP GLN VAL VAL THR ALA ARG LEU ASN GLN LEU SEQRES 39 B 510 GLU ARG ASP ALA ALA ASP GLY TRP GLU GLU ALA ARG GLY SEQRES 40 B 510 PHE LEU ARG HET SF4 A 501 8 HET MET B 501 9 HET SF4 B 502 8 HETNAM SF4 IRON/SULFUR CLUSTER HETNAM MET METHIONINE FORMUL 3 SF4 2(FE4 S4) FORMUL 4 MET C5 H11 N O2 S FORMUL 6 HOH *697(H2 O) HELIX 1 AA1 ALA A 10 CYS A 15 5 6 HELIX 2 AA2 ASP A 21 GLY A 36 1 16 HELIX 3 AA3 PRO A 40 GLY A 59 1 20 HELIX 4 AA4 PRO A 65 GLY A 74 1 10 HELIX 5 AA5 ASP A 76 GLY A 88 1 13 HELIX 6 AA6 VAL A 90 THR A 99 1 10 HELIX 7 AA7 ALA A 102 THR A 109 1 8 HELIX 8 AA8 THR A 109 ARG A 116 1 8 HELIX 9 AA9 GLY A 117 ALA A 124 1 8 HELIX 10 AB1 ASP A 157 SER A 159 5 3 HELIX 11 AB2 ALA A 160 ASP A 173 1 14 HELIX 12 AB3 GLU A 190 ASN A 194 5 5 HELIX 13 AB4 GLY A 196 HIS A 207 1 12 HELIX 14 AB5 THR A 221 GLN A 228 1 8 HELIX 15 AB6 PRO A 229 LEU A 234 5 6 HELIX 16 AB7 ASN A 245 GLY A 254 1 10 HELIX 17 AB8 ALA A 257 GLU A 277 1 21 HELIX 18 AB9 SER A 294 GLY A 310 1 17 HELIX 19 AC1 GLU A 339 THR A 355 1 17 HELIX 20 AC2 GLY A 363 ARG A 370 1 8 HELIX 21 AC3 LYS A 381 MET A 385 5 5 HELIX 22 AC4 GLY A 416 ARG A 419 5 4 HELIX 23 AC5 SER A 430 ARG A 441 1 12 HELIX 24 AC6 GLY A 450 MET A 455 5 6 HELIX 25 AC7 ASP A 456 ASP A 475 1 20 HELIX 26 AC8 ALA B 10 ARG B 14 5 5 HELIX 27 AC9 ASP B 21 ALA B 35 1 15 HELIX 28 AD1 PRO B 40 SER B 61 1 22 HELIX 29 AD2 PRO B 65 GLY B 74 1 10 HELIX 30 AD3 ASP B 76 GLY B 88 1 13 HELIX 31 AD4 VAL B 90 THR B 99 1 10 HELIX 32 AD5 ALA B 102 THR B 109 1 8 HELIX 33 AD6 THR B 109 ARG B 116 1 8 HELIX 34 AD7 GLY B 117 ALA B 124 1 8 HELIX 35 AD8 CYS B 148 GLY B 153 5 6 HELIX 36 AD9 ASP B 157 SER B 159 5 3 HELIX 37 AE1 ALA B 160 ILE B 175 1 16 HELIX 38 AE2 GLU B 190 ASN B 194 5 5 HELIX 39 AE3 GLY B 196 HIS B 207 1 12 HELIX 40 AE4 THR B 221 GLN B 228 1 8 HELIX 41 AE5 PRO B 229 LEU B 234 5 6 HELIX 42 AE6 ASN B 245 GLY B 254 1 10 HELIX 43 AE7 ALA B 257 GLU B 277 1 21 HELIX 44 AE8 ARG B 292 SER B 294 5 3 HELIX 45 AE9 ARG B 295 GLY B 310 1 16 HELIX 46 AF1 ALA B 338 THR B 355 1 18 HELIX 47 AF2 GLY B 363 THR B 371 1 9 HELIX 48 AF3 LYS B 381 MET B 385 5 5 HELIX 49 AF4 TYR B 406 GLY B 410 5 5 HELIX 50 AF5 GLY B 416 ARG B 419 5 4 HELIX 51 AF6 SER B 430 ARG B 441 1 12 HELIX 52 AF7 GLY B 450 MET B 455 5 6 HELIX 53 AF8 ASP B 456 ASP B 475 1 20 SHEET 1 AA1 5 MET A 183 PHE A 185 0 SHEET 2 AA1 5 SER A 132 TYR A 136 1 N LEU A 135 O TYR A 184 SHEET 3 AA1 5 ALA A 394 ASP A 398 1 O VAL A 397 N TYR A 136 SHEET 4 AA1 5 ASP A 402 TYR A 404 -1 O TYR A 404 N GLN A 396 SHEET 5 AA1 5 ILE A 421 ARG A 424 -1 O GLY A 423 N VAL A 403 SHEET 1 AA2 5 THR A 212 THR A 215 0 SHEET 2 AA2 5 ALA A 236 LEU A 241 1 O SER A 240 N THR A 215 SHEET 3 AA2 5 ASN A 281 VAL A 288 1 O ALA A 285 N LEU A 241 SHEET 4 AA2 5 PHE A 317 GLU A 322 1 O ASN A 319 N PHE A 284 SHEET 5 AA2 5 HIS A 359 TYR A 362 1 O ASP A 361 N VAL A 318 SHEET 1 AA3 5 MET B 183 PHE B 185 0 SHEET 2 AA3 5 SER B 132 LEU B 135 1 N LEU B 135 O TYR B 184 SHEET 3 AA3 5 ALA B 394 VAL B 397 1 O VAL B 397 N GLY B 134 SHEET 4 AA3 5 ASP B 402 TYR B 404 -1 O TYR B 404 N GLN B 396 SHEET 5 AA3 5 ILE B 421 ARG B 424 -1 O GLY B 423 N VAL B 403 SHEET 1 AA4 5 THR B 212 THR B 215 0 SHEET 2 AA4 5 ALA B 236 LEU B 241 1 O SER B 240 N THR B 215 SHEET 3 AA4 5 ASN B 281 ILE B 287 1 O ALA B 285 N LEU B 241 SHEET 4 AA4 5 PHE B 317 ARG B 321 1 O ASN B 319 N PHE B 284 SHEET 5 AA4 5 HIS B 359 TYR B 362 1 O ASP B 361 N VAL B 318 LINK SG CYS A 141 FE1 SF4 A 501 1555 1555 2.50 LINK SG CYS A 145 FE2 SF4 A 501 1555 1555 2.67 LINK FE4 SF4 A 501 O HOH A 625 1555 1555 2.65 LINK SG CYS B 141 FE4 SF4 B 502 1555 1555 2.52 LINK SG CYS B 145 FE2 SF4 B 502 1555 1555 2.62 LINK SG CYS B 148 FE1 SF4 B 502 1555 1555 2.64 CRYST1 97.088 105.190 118.248 90.00 90.00 90.00 P 21 2 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 0.010300 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009507 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008457 0.00000