HEADER OXIDOREDUCTASE 21-NOV-25 9TCD TITLE XFEL STRUCTURE OF OXIDISED RIBONUCLEOTIDE REDUCTASE R2A Y122F MUTANT TITLE 2 FROM E. COLI, HEXAGONAL P6122 FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN B2,PROTEIN R2,RIBONUCLEOTIDE REDUCTASE 1; COMPND 5 EC: 1.17.4.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: NRDB, FTSB, B2235, JW2229; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS RIBONUCLEOTIDE REDUCTASE BETA SUBUNIT, R2A, DI-IRON BETA SUBUNIT, KEYWDS 2 XFEL STRUCTURE, OXIDOREDUCTASE, P6122 EXPDTA X-RAY DIFFRACTION AUTHOR R.KUMAR,V.SRINIVAS,M.HOGBOM REVDAT 1 13-MAY-26 9TCD 0 JRNL AUTH L.PACOSTE,R.KUMAR,V.SRINIVAS,H.MAKITA,P.S.SIMON,R.BANNERJEE, JRNL AUTH 2 N.M.MINNETIAN,A.BHOWMICK,D.W.PALEY,D.W.MITTAN-MOREAU, JRNL AUTH 3 K.CHATTERJEE,D.J.ROSENBERG,A.BATYUK,L.B.GEE,R.ALONSO-MORI, JRNL AUTH 4 N.K.SAUTER,J.YANO,V.K.YACHANDRA,J.JOHN,O.AURELIUS, JRNL AUTH 5 A.S.BREWSTER,J.F.KERN,B.BLOMBERG,H.LEBRETTE,H.XU,G.HOFER, JRNL AUTH 6 M.HOGBOM,X.ZOU JRNL TITL TRACKING THE REDOX REACTION OF THE IRON ENZYME JRNL TITL 2 RIBONUCLEOTIDE REDUCTASE USING CONTINUOUS SERIALED AND SFX JRNL REF STRUCTURE 2026 JRNL REFN ISSN 0969-2126 JRNL DOI 10.1016/J.STR.2026.03.006 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 14829 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1482 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 22.7800 - 5.9700 0.98 1350 150 0.1711 0.1875 REMARK 3 2 5.9700 - 4.7500 0.99 1259 140 0.1907 0.1984 REMARK 3 3 4.7500 - 4.1600 0.97 1214 135 0.1662 0.2175 REMARK 3 4 4.1600 - 3.7800 0.93 1150 128 0.2028 0.2282 REMARK 3 5 3.7800 - 3.5100 0.93 1138 126 0.2341 0.2996 REMARK 3 6 3.5100 - 3.3000 0.98 1195 134 0.2389 0.2935 REMARK 3 7 3.3000 - 3.1400 1.00 1218 135 0.2546 0.3441 REMARK 3 8 3.1400 - 3.0000 1.00 1208 134 0.3256 0.3672 REMARK 3 9 3.0000 - 2.8900 1.00 1214 135 0.3199 0.3120 REMARK 3 10 2.8900 - 2.7900 1.00 1196 133 0.3303 0.3857 REMARK 3 11 2.7900 - 2.7000 1.00 1205 132 0.4310 0.4721 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) : 0.401 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.835 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 62.61 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 87.21 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 : 0.004 2880 REMARK 3 ANGLE : 0.618 3912 REMARK 3 CHIRALITY : 0.041 433 REMARK 3 PLANARITY : 0.015 503 REMARK 3 DIHEDRAL : 15.233 1073 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 129 ) REMARK 3 ORIGIN FOR THE GROUP (A): 33.6796 -39.0822 22.9993 REMARK 3 T TENSOR REMARK 3 T11: 0.4170 T22: 0.7558 REMARK 3 T33: 0.5639 T12: -0.2357 REMARK 3 T13: 0.0031 T23: 0.0883 REMARK 3 L TENSOR REMARK 3 L11: 1.0381 L22: 2.5308 REMARK 3 L33: 1.9421 L12: -1.0504 REMARK 3 L13: 0.8261 L23: -1.2079 REMARK 3 S TENSOR REMARK 3 S11: -0.0793 S12: -0.4112 S13: -0.1499 REMARK 3 S21: -0.2146 S22: 0.4918 S23: 0.3192 REMARK 3 S31: 0.2596 S32: -0.7599 S33: -0.3043 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 130 THROUGH 205 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.1376 -51.4570 25.8308 REMARK 3 T TENSOR REMARK 3 T11: 0.7827 T22: 1.3348 REMARK 3 T33: 1.1095 T12: -0.4125 REMARK 3 T13: -0.0675 T23: 0.4839 REMARK 3 L TENSOR REMARK 3 L11: 2.3220 L22: 0.5506 REMARK 3 L33: 0.9603 L12: -0.3386 REMARK 3 L13: -0.4442 L23: 0.5888 REMARK 3 S TENSOR REMARK 3 S11: 0.0709 S12: -0.1504 S13: -0.6777 REMARK 3 S21: -0.2259 S22: 0.3407 S23: 0.8263 REMARK 3 S31: 0.9636 S32: -0.9710 S33: 0.1371 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 206 THROUGH 268 ) REMARK 3 ORIGIN FOR THE GROUP (A): 36.0154 -42.0074 33.9477 REMARK 3 T TENSOR REMARK 3 T11: 0.4946 T22: 0.9595 REMARK 3 T33: 0.4241 T12: -0.0983 REMARK 3 T13: 0.0193 T23: 0.0053 REMARK 3 L TENSOR REMARK 3 L11: 0.6514 L22: 3.6819 REMARK 3 L33: 1.6890 L12: -1.3048 REMARK 3 L13: -0.6222 L23: 0.0251 REMARK 3 S TENSOR REMARK 3 S11: -0.2177 S12: -0.5194 S13: -0.1527 REMARK 3 S21: 0.2272 S22: 0.4227 S23: 0.1467 REMARK 3 S31: 0.1545 S32: -0.6879 S33: -0.1069 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 269 THROUGH 341 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.2055 -51.6087 41.4119 REMARK 3 T TENSOR REMARK 3 T11: 0.6095 T22: 1.1288 REMARK 3 T33: 0.5632 T12: -0.1230 REMARK 3 T13: 0.0272 T23: 0.2577 REMARK 3 L TENSOR REMARK 3 L11: 6.6090 L22: 2.7485 REMARK 3 L33: 2.4771 L12: -2.0031 REMARK 3 L13: -2.0476 L23: 0.9276 REMARK 3 S TENSOR REMARK 3 S11: -0.2039 S12: -0.8072 S13: -0.4604 REMARK 3 S21: 0.2122 S22: 0.5059 S23: 0.5328 REMARK 3 S31: 0.2690 S32: -0.4045 S33: -0.2963 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 9TCD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-NOV-25. REMARK 100 THE DEPOSITION ID IS D_1292152387. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUL-21 REMARK 200 TEMPERATURE (KELVIN) : 297 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : FREE ELECTRON LASER REMARK 200 BEAMLINE : MFX REMARK 200 X-RAY GENERATOR MODEL : SLAC LCLS BEAMLINE MFX REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.304826 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX340-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CCTBX.XFEL REMARK 200 DATA SCALING SOFTWARE : CXI.MERGE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14829 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 22.780 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 1011. REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.5900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.79 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 : 2.270 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4M SODIUM FORMATE, BATCH MODE, REMARK 280 TEMPERATURE 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 67.86367 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 135.72733 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 101.79550 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 169.65917 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 33.93183 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 67.86367 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 135.72733 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 169.65917 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 101.79550 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 33.93183 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 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 0.500000 0.866025 0.000000 46.75400 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -80.98030 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 33.93183 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 ASP A 342 REMARK 465 ASN A 343 REMARK 465 VAL A 344 REMARK 465 GLN A 345 REMARK 465 VAL A 346 REMARK 465 ALA A 347 REMARK 465 PRO A 348 REMARK 465 GLN A 349 REMARK 465 GLU A 350 REMARK 465 VAL A 351 REMARK 465 GLU A 352 REMARK 465 VAL A 353 REMARK 465 SER A 354 REMARK 465 SER A 355 REMARK 465 TYR A 356 REMARK 465 LEU A 357 REMARK 465 VAL A 358 REMARK 465 GLY A 359 REMARK 465 GLN A 360 REMARK 465 ILE A 361 REMARK 465 ASP A 362 REMARK 465 SER A 363 REMARK 465 GLU A 364 REMARK 465 VAL A 365 REMARK 465 ASP A 366 REMARK 465 THR A 367 REMARK 465 ASP A 368 REMARK 465 ASP A 369 REMARK 465 LEU A 370 REMARK 465 SER A 371 REMARK 465 ASN A 372 REMARK 465 PHE A 373 REMARK 465 GLN A 374 REMARK 465 LEU A 375 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 O HIS A 241 O HOH A 501 2.19 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 5 103.04 -162.24 REMARK 500 ASN A 24 -72.64 -104.73 REMARK 500 ILE A 206 -56.76 -121.23 REMARK 500 PHE A 291 33.02 -98.81 REMARK 500 SER A 295 -166.24 -105.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 328 0.19 SIDE CHAIN 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 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 84 OD1 REMARK 620 2 ASP A 84 OD2 48.3 REMARK 620 3 GLU A 115 OE1 64.5 90.6 REMARK 620 4 HIS A 118 ND1 131.4 85.0 111.3 REMARK 620 5 HOH A 502 O 121.3 153.0 107.0 106.5 REMARK 620 6 HOH A 504 O 70.9 62.9 134.9 102.3 90.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 402 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 115 OE2 REMARK 620 2 GLU A 204 OE2 87.5 REMARK 620 3 GLU A 238 OE1 148.8 96.7 REMARK 620 4 HIS A 241 ND1 108.1 99.9 101.7 REMARK 620 5 HOH A 502 O 88.0 170.3 82.8 89.7 REMARK 620 6 HOH A 503 O 66.1 83.3 83.6 173.4 87.0 REMARK 620 N 1 2 3 4 5 DBREF 9TCD A 1 375 UNP P69924 RIR2_ECOLI 2 376 SEQADV 9TCD PHE A 122 UNP P69924 TYR 123 ENGINEERED MUTATION SEQRES 1 A 375 ALA TYR THR THR PHE SER GLN THR LYS ASN ASP GLN LEU SEQRES 2 A 375 LYS GLU PRO MET PHE PHE GLY GLN PRO VAL ASN VAL ALA SEQRES 3 A 375 ARG TYR ASP GLN GLN LYS TYR ASP ILE PHE GLU LYS LEU SEQRES 4 A 375 ILE GLU LYS GLN LEU SER PHE PHE TRP ARG PRO GLU GLU SEQRES 5 A 375 VAL ASP VAL SER ARG ASP ARG ILE ASP TYR GLN ALA LEU SEQRES 6 A 375 PRO GLU HIS GLU LYS HIS ILE PHE ILE SER ASN LEU LYS SEQRES 7 A 375 TYR GLN THR LEU LEU ASP SER ILE GLN GLY ARG SER PRO SEQRES 8 A 375 ASN VAL ALA LEU LEU PRO LEU ILE SER ILE PRO GLU LEU SEQRES 9 A 375 GLU THR TRP VAL GLU THR TRP ALA PHE SER GLU THR ILE SEQRES 10 A 375 HIS SER ARG SER PHE THR HIS ILE ILE ARG ASN ILE VAL SEQRES 11 A 375 ASN ASP PRO SER VAL VAL PHE ASP ASP ILE VAL THR ASN SEQRES 12 A 375 GLU GLN ILE GLN LYS ARG ALA GLU GLY ILE SER SER TYR SEQRES 13 A 375 TYR ASP GLU LEU ILE GLU MET THR SER TYR TRP HIS LEU SEQRES 14 A 375 LEU GLY GLU GLY THR HIS THR VAL ASN GLY LYS THR VAL SEQRES 15 A 375 THR VAL SER LEU ARG GLU LEU LYS LYS LYS LEU TYR LEU SEQRES 16 A 375 CYS LEU MET SER VAL ASN ALA LEU GLU ALA ILE ARG PHE SEQRES 17 A 375 TYR VAL SER PHE ALA CYS SER PHE ALA PHE ALA GLU ARG SEQRES 18 A 375 GLU LEU MET GLU GLY ASN ALA LYS ILE ILE ARG LEU ILE SEQRES 19 A 375 ALA ARG ASP GLU ALA LEU HIS LEU THR GLY THR GLN HIS SEQRES 20 A 375 MET LEU ASN LEU LEU ARG SER GLY ALA ASP ASP PRO GLU SEQRES 21 A 375 MET ALA GLU ILE ALA GLU GLU CYS LYS GLN GLU CYS TYR SEQRES 22 A 375 ASP LEU PHE VAL GLN ALA ALA GLN GLN GLU LYS ASP TRP SEQRES 23 A 375 ALA ASP TYR LEU PHE ARG ASP GLY SER MET ILE GLY LEU SEQRES 24 A 375 ASN LYS ASP ILE LEU CYS GLN TYR VAL GLU TYR ILE THR SEQRES 25 A 375 ASN ILE ARG MET GLN ALA VAL GLY LEU ASP LEU PRO PHE SEQRES 26 A 375 GLN THR ARG SER ASN PRO ILE PRO TRP ILE ASN THR TRP SEQRES 27 A 375 LEU VAL SER ASP ASN VAL GLN VAL ALA PRO GLN GLU VAL SEQRES 28 A 375 GLU VAL SER SER TYR LEU VAL GLY GLN ILE ASP SER GLU SEQRES 29 A 375 VAL ASP THR ASP ASP LEU SER ASN PHE GLN LEU HET FE A 401 1 HET FE A 402 1 HETNAM FE FE (III) ION FORMUL 2 FE 2(FE 3+) FORMUL 4 HOH *8(H2 O) HELIX 1 AA1 ASP A 11 GLU A 15 5 5 HELIX 2 AA2 TYR A 33 PHE A 46 1 14 HELIX 3 AA3 ARG A 49 VAL A 53 5 5 HELIX 4 AA4 VAL A 55 LEU A 65 1 11 HELIX 5 AA5 PRO A 66 LEU A 95 1 30 HELIX 6 AA6 LEU A 96 ILE A 99 5 4 HELIX 7 AA7 ILE A 101 VAL A 130 1 30 HELIX 8 AA8 ASP A 132 VAL A 141 1 10 HELIX 9 AA9 ASN A 143 GLY A 171 1 29 HELIX 10 AB1 SER A 185 ILE A 206 1 22 HELIX 11 AB2 ILE A 206 ARG A 221 1 16 HELIX 12 AB3 MET A 224 SER A 254 1 31 HELIX 13 AB4 ASP A 258 CYS A 268 1 11 HELIX 14 AB5 CYS A 268 PHE A 291 1 24 HELIX 15 AB6 ASN A 300 VAL A 319 1 20 HELIX 16 AB7 TRP A 334 LEU A 339 1 6 SHEET 1 AA1 2 GLY A 173 VAL A 177 0 SHEET 2 AA1 2 LYS A 180 VAL A 184 -1 O LYS A 180 N VAL A 177 LINK OD1 ASP A 84 FE FE A 401 1555 1555 2.65 LINK OD2 ASP A 84 FE FE A 401 1555 1555 2.72 LINK OE1 GLU A 115 FE FE A 401 1555 1555 2.55 LINK OE2 GLU A 115 FE FE A 402 1555 1555 2.15 LINK ND1 HIS A 118 FE FE A 401 1555 1555 2.10 LINK OE2 GLU A 204 FE FE A 402 1555 1555 1.79 LINK OE1 GLU A 238 FE FE A 402 1555 1555 1.79 LINK ND1 HIS A 241 FE FE A 402 1555 1555 2.34 LINK FE FE A 401 O HOH A 502 1555 1555 1.86 LINK FE FE A 401 O HOH A 504 1555 1555 2.19 LINK FE FE A 402 O HOH A 502 1555 1555 1.73 LINK FE FE A 402 O HOH A 503 1555 1555 2.31 CRYST1 93.508 93.508 203.591 90.00 90.00 120.00 P 61 2 2 12 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 0.010694 0.006174 0.000000 0.00000 SCALE2 0.000000 0.012349 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004912 0.00000 CONECT 726 2814 CONECT 727 2814 CONECT 972 2814 CONECT 973 2815 CONECT 995 2814 CONECT 1690 2815 CONECT 1976 2815 CONECT 1997 2815 CONECT 2814 726 727 972 995 CONECT 2814 2817 2819 CONECT 2815 973 1690 1976 1997 CONECT 2815 2817 2818 CONECT 2817 2814 2815 CONECT 2818 2815 CONECT 2819 2814 MASTER 407 0 2 16 2 0 0 6 2803 1 15 29 END