HEADER OXIDOREDUCTASE 21-JAN-20 6XV4 TITLE NEUTRON STRUCTURE OF FERRIC ASCORBATE PEROXIDASE-ASCORBATE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: ASCORBATE PEROXIDASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYTOSOLIC ASCORBATE PEROXIDASE 1,UNCHARACTERIZED PROTEIN; COMPND 5 EC: 1.11.1.11; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GLYCINE MAX; SOURCE 3 ORGANISM_COMMON: SOYBEAN; SOURCE 4 ORGANISM_TAXID: 3847; SOURCE 5 GENE: APX1, GLYMA_U021900; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ASCORBATE PEROXIDASE, NEUTRON CRYSTALLOGRAPHY, HEME PEROXIDASE, KEYWDS 2 PROTON PATHWAY, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION; NEUTRON DIFFRACTION AUTHOR H.KWON,J.BASRAN,J.M.DEVOS,T.E.SCHRADER,A.OSTERMANN,M.P.BLAKELEY, AUTHOR 2 E.L.RAVEN,P.C.E.MOODY REVDAT 3 29-JUL-20 6XV4 1 REMARK SITE REVDAT 2 08-APR-20 6XV4 1 JRNL REVDAT 1 18-MAR-20 6XV4 0 JRNL AUTH H.KWON,J.BASRAN,J.M.DEVOS,R.SUARDIAZ,M.W.VAN DER KAMP, JRNL AUTH 2 A.J.MULHOLLAND,T.E.SCHRADER,A.OSTERMANN,M.P.BLAKELEY, JRNL AUTH 3 P.C.E.MOODY,E.L.RAVEN JRNL TITL VISUALIZING THE PROTONS IN A METALLOENZYME ELECTRON PROTON JRNL TITL 2 TRANSFER PATHWAY. JRNL REF PROC.NATL.ACAD.SCI.USA V. 117 6484 2020 JRNL REFN ESSN 1091-6490 JRNL PMID 32152099 JRNL DOI 10.1073/PNAS.1918936117 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 X-RAY DATA. REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 20642 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2065 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 4.6700 - 3.7100 1.00 1277 141 0.1515 0.1901 REMARK 3 2 3.7100 - 3.2500 1.00 1261 141 0.1525 0.2084 REMARK 3 3 3.2500 - 2.9500 1.00 1249 137 0.1754 0.2438 REMARK 3 4 2.9500 - 2.7400 1.00 1240 138 0.1680 0.2462 REMARK 3 5 2.7400 - 2.5800 1.00 1226 135 0.1673 0.2310 REMARK 3 6 2.5800 - 2.4500 1.00 1234 139 0.1531 0.2224 REMARK 3 7 2.4500 - 2.3400 1.00 1213 134 0.1530 0.2330 REMARK 3 8 2.3400 - 2.2500 1.00 1227 137 0.1555 0.2360 REMARK 3 9 2.2500 - 2.1700 1.00 1219 135 0.1715 0.2297 REMARK 3 10 2.1700 - 2.1100 1.00 1216 135 0.1553 0.2206 REMARK 3 11 2.1100 - 2.0500 1.00 1222 136 0.1555 0.2315 REMARK 3 12 2.0500 - 1.9900 1.00 1213 134 0.1650 0.2276 REMARK 3 13 1.9900 - 1.9400 1.00 1201 134 0.1770 0.2181 REMARK 3 14 1.9400 - 1.9000 1.00 1221 136 0.1898 0.2229 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.980 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.63 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 : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 3 NEUTRON DATA. REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.3 REMARK 3 NUMBER OF REFLECTIONS : 14348 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.298 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1435 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 4.4900 - 3.5700 0.99 1438 160 0.1626 0.2519 REMARK 3 2 3.5600 - 3.1200 0.98 1396 155 0.1909 0.2922 REMARK 3 3 3.1200 - 2.8300 0.95 1336 149 0.2223 0.3056 REMARK 3 4 2.8300 - 2.6300 0.90 1261 139 0.2165 0.3043 REMARK 3 5 2.6300 - 2.4700 0.91 1259 141 0.2202 0.3080 REMARK 3 6 2.4700 - 2.3500 0.89 1238 137 0.2193 0.2920 REMARK 3 7 2.3500 - 2.2500 0.85 1193 133 0.2196 0.3242 REMARK 3 8 2.2500 - 2.1600 0.83 1146 127 0.2288 0.3102 REMARK 3 9 2.1600 - 2.0900 0.81 1115 124 0.2425 0.3459 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.980 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : NULL 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 6XV4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1292106358. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 200678 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.90 REMARK 200 R MERGE (I) : 0.20000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.60000 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: 5JPR REMARK 200 REMARK 200 REMARK: NULL REMARK 230 REMARK 230 EXPERIMENTAL DETAILS REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION REMARK 230 DATE OF DATA COLLECTION : 01-FEB-17 REMARK 230 TEMPERATURE (KELVIN) : 100.0 REMARK 230 PH : NULL REMARK 230 NUMBER OF CRYSTALS USED : 1 REMARK 230 REMARK 230 NEUTRON SOURCE : NUCLEAR REACTOR REMARK 230 BEAMLINE : BIODIFF REMARK 230 WAVELENGTH OR RANGE (A) : 3.4 REMARK 230 MONOCHROMATOR : NULL REMARK 230 OPTICS : NULL REMARK 230 REMARK 230 DETECTOR TYPE : IMAGE PLATE REMARK 230 DETECTOR MANUFACTURER : BIODIFF REMARK 230 INTENSITY-INTEGRATION SOFTWARE : AIMLESS REMARK 230 DATA SCALING SOFTWARE : AIMLESS REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 14368 REMARK 230 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 230 RESOLUTION RANGE LOW (A) : 36.200 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 91.1 REMARK 230 DATA REDUNDANCY : 3.000 REMARK 230 R MERGE (I) : 0.20000 REMARK 230 R SYM (I) : NULL REMARK 230 FOR THE DATA SET : 3.9000 REMARK 230 REMARK 230 IN THE HIGHEST RESOLUTION SHELL. REMARK 230 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 230 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 230 COMPLETENESS FOR SHELL (%) : NULL REMARK 230 DATA REDUNDANCY IN SHELL : NULL REMARK 230 R MERGE FOR SHELL (I) : 0.40000 REMARK 230 R SYM FOR SHELL (I) : NULL REMARK 230 FOR SHELL : NULL REMARK 230 REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 230 SOFTWARE USED : PHASER REMARK 230 STARTING MODEL: 5JPR REMARK 230 REMARK 230 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: LITHIUM SULFATE HEPES, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 300K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 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 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 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 0.000000 -1.000000 0.000000 40.93100 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 40.93100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.48450 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 40.93100 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 40.93100 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.48450 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 40.93100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.93100 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 37.48450 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 40.93100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.93100 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.48450 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 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: 4280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -96.0 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 163.72400 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 -163.72400 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 O DOD A 421 LIES ON A SPECIAL POSITION. REMARK 375 O DOD A 436 LIES ON A SPECIAL POSITION. REMARK 375 O DOD A 607 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -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 ALA A 250 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 DZ2 LYS A 20 O DOD A 418 1.57 REMARK 500 D HIS A 140 O3 SO4 A 304 1.59 REMARK 500 O DOD A 658 O DOD A 709 1.76 REMARK 500 O DOD A 617 O DOD A 659 1.95 REMARK 500 OE2 GLU A 198 O DOD A 401 1.96 REMARK 500 OE1 GLN A 13 O DOD A 402 1.98 REMARK 500 NZ LYS A 18 O DOD A 403 2.03 REMARK 500 OE1 GLU A 112 O DOD A 404 2.03 REMARK 500 O DOD A 647 O DOD A 687 2.08 REMARK 500 OE1 GLU A 82 O DOD A 405 2.08 REMARK 500 O2 SO4 A 304 O DOD A 406 2.08 REMARK 500 O DOD A 642 O DOD A 670 2.09 REMARK 500 OE1 GLU A 128 O DOD A 407 2.09 REMARK 500 OG SER A 43 O DOD A 408 2.09 REMARK 500 O DOD A 612 O DOD A 679 2.09 REMARK 500 O DOD A 690 O DOD A 737 2.11 REMARK 500 O DOD A 672 O DOD A 713 2.12 REMARK 500 O DOD A 757 O DOD A 763 2.12 REMARK 500 O DOD A 654 O DOD A 677 2.13 REMARK 500 O DOD A 509 O DOD A 714 2.17 REMARK 500 O DOD A 427 O DOD A 568 2.19 REMARK 500 O4 SO4 A 304 O DOD A 409 2.19 REMARK 500 O DOD A 530 O DOD A 658 2.19 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 DOD A 424 O DOD A 424 2965 1.70 REMARK 500 O DOD A 684 O DOD A 684 2965 2.13 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 38 NE ARG A 38 CZ 0.125 REMARK 500 ARG A 38 CZ ARG A 38 NH1 0.135 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 38 NE - CZ - NH1 ANGL. DEV. = -4.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA A 148 -70.74 -85.63 REMARK 500 ARG A 172 -82.48 -104.89 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 DOD A 761 DISTANCE = 5.83 ANGSTROMS REMARK 525 DOD A 762 DISTANCE = 5.86 ANGSTROMS REMARK 525 DOD A 763 DISTANCE = 6.15 ANGSTROMS REMARK 525 DOD A 764 DISTANCE = 7.36 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 HEM A 301 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 163 NE2 REMARK 620 2 HEM A 301 NA 93.1 REMARK 620 3 HEM A 301 NB 92.8 88.7 REMARK 620 4 HEM A 301 NC 90.2 176.3 92.8 REMARK 620 5 HEM A 301 ND 93.6 86.5 172.1 91.7 REMARK 620 6 DOD A 465 O 175.8 82.8 88.3 93.8 85.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 302 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 164 O REMARK 620 2 THR A 164 OG1 66.1 REMARK 620 3 THR A 180 OG1 69.3 106.3 REMARK 620 4 ASN A 182 O 89.8 154.2 71.2 REMARK 620 5 ASN A 182 OD1 140.2 139.7 73.3 65.4 REMARK 620 6 ILE A 185 O 84.0 92.9 136.0 74.6 115.7 REMARK 620 7 ASP A 187 OD1 126.6 62.2 137.9 136.9 90.6 86.1 REMARK 620 N 1 2 3 4 5 6 DBREF 6XV4 A 2 250 UNP Q43758 Q43758_SOYBN 2 250 SEQADV 6XV4 MET A -10 UNP Q43758 INITIATING METHIONINE SEQADV 6XV4 ARG A -9 UNP Q43758 EXPRESSION TAG SEQADV 6XV4 GLY A -8 UNP Q43758 EXPRESSION TAG SEQADV 6XV4 SER A -7 UNP Q43758 EXPRESSION TAG SEQADV 6XV4 HIS A -6 UNP Q43758 EXPRESSION TAG SEQADV 6XV4 HIS A -5 UNP Q43758 EXPRESSION TAG SEQADV 6XV4 HIS A -4 UNP Q43758 EXPRESSION TAG SEQADV 6XV4 HIS A -3 UNP Q43758 EXPRESSION TAG SEQADV 6XV4 HIS A -2 UNP Q43758 EXPRESSION TAG SEQADV 6XV4 HIS A -1 UNP Q43758 EXPRESSION TAG SEQADV 6XV4 GLY A 0 UNP Q43758 EXPRESSION TAG SEQADV 6XV4 SER A 1 UNP Q43758 EXPRESSION TAG SEQRES 1 A 261 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER GLY SEQRES 2 A 261 LYS SER TYR PRO THR VAL SER ALA ASP TYR GLN LYS ALA SEQRES 3 A 261 VAL GLU LYS ALA LYS LYS LYS LEU ARG GLY PHE ILE ALA SEQRES 4 A 261 GLU LYS ARG CYS ALA PRO LEU MET LEU ARG LEU ALA TRP SEQRES 5 A 261 HIS SER ALA GLY THR PHE ASP LYS GLY THR LYS THR GLY SEQRES 6 A 261 GLY PRO PHE GLY THR ILE LYS HIS PRO ALA GLU LEU ALA SEQRES 7 A 261 HIS SER ALA ASN ASN GLY LEU ASP ILE ALA VAL ARG LEU SEQRES 8 A 261 LEU GLU PRO LEU LYS ALA GLU PHE PRO ILE LEU SER TYR SEQRES 9 A 261 ALA ASP PHE TYR GLN LEU ALA GLY VAL VAL ALA VAL GLU SEQRES 10 A 261 VAL THR GLY GLY PRO GLU VAL PRO PHE HIS PRO GLY ARG SEQRES 11 A 261 GLU ASP LYS PRO GLU PRO PRO PRO GLU GLY ARG LEU PRO SEQRES 12 A 261 ASP ALA THR LYS GLY SER ASP HIS LEU ARG ASP VAL PHE SEQRES 13 A 261 GLY LYS ALA MET GLY LEU THR ASP GLN ASP ILE VAL ALA SEQRES 14 A 261 LEU SER GLY GLY HIS THR ILE GLY ALA ALA HIS LYS GLU SEQRES 15 A 261 ARG SER GLY PHE GLU GLY PRO TRP THR SER ASN PRO LEU SEQRES 16 A 261 ILE PHE ASP ASN SER TYR PHE THR GLU LEU LEU SER GLY SEQRES 17 A 261 GLU LYS GLU GLY LEU LEU GLN LEU PRO SER ASP LYS ALA SEQRES 18 A 261 LEU LEU SER ASP PRO VAL PHE ARG PRO LEU VAL ASP LYS SEQRES 19 A 261 TYR ALA ALA ASP GLU ASP ALA PHE PHE ALA ASP TYR ALA SEQRES 20 A 261 GLU ALA HIS GLN LYS LEU SER GLU LEU GLY PHE ALA ASP SEQRES 21 A 261 ALA HET HEM A 301 73 HET K A 302 1 HET SO4 A 303 5 HET SO4 A 304 5 HET ASC A 305 19 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM K POTASSIUM ION HETNAM SO4 SULFATE ION HETNAM ASC ASCORBIC ACID HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 K K 1+ FORMUL 4 SO4 2(O4 S 2-) FORMUL 6 ASC C6 H8 O6 FORMUL 7 DOD *364(D2 O) HELIX 1 AA1 SER A 9 ARG A 31 1 23 HELIX 2 AA2 CYS A 32 GLY A 45 1 14 HELIX 3 AA3 GLY A 58 LYS A 61 5 4 HELIX 4 AA4 HIS A 62 ALA A 67 1 6 HELIX 5 AA5 HIS A 68 ASN A 72 5 5 HELIX 6 AA6 GLY A 73 GLU A 87 1 15 HELIX 7 AA7 SER A 92 THR A 108 1 17 HELIX 8 AA8 GLY A 137 GLY A 146 1 10 HELIX 9 AA9 THR A 152 GLY A 161 1 10 HELIX 10 AB1 GLY A 162 ILE A 165 5 4 HELIX 11 AB2 ASN A 188 GLY A 197 1 10 HELIX 12 AB3 LEU A 205 ASP A 214 1 10 HELIX 13 AB4 VAL A 216 ASP A 227 1 12 HELIX 14 AB5 ASP A 227 GLU A 244 1 18 SHEET 1 AA1 2 ALA A 167 ALA A 168 0 SHEET 2 AA1 2 GLY A 177 PRO A 178 -1 O GLY A 177 N ALA A 168 LINK NE2 HIS A 163 FE HEM A 301 1555 1555 2.14 LINK O THR A 164 K K A 302 1555 1555 2.59 LINK OG1 THR A 164 K K A 302 1555 1555 3.00 LINK OG1 THR A 180 K K A 302 1555 1555 2.90 LINK O ASN A 182 K K A 302 1555 1555 2.91 LINK OD1 ASN A 182 K K A 302 1555 1555 2.81 LINK O ILE A 185 K K A 302 1555 1555 2.65 LINK OD1 ASP A 187 K K A 302 1555 1555 2.99 LINK FE HEM A 301 O DOD A 465 1555 1555 2.25 CRYST1 81.862 81.862 74.969 90.00 90.00 90.00 P 42 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 0.012216 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012216 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013339 0.00000