HEADER HYDROLASE 03-MAR-11 2YBD TITLE CRYSTAL STRUCTURE OF PROBABLE HAD FAMILY HYDROLASE FROM PSEUDOMONAS TITLE 2 FLUORESCENS PF-5 WITH BOUND PHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYDROLASE, HALOACID DEHALOGENASE-LIKE FAMILY; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS FLUORESCENS PF-5; SOURCE 3 ORGANISM_TAXID: 220664; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE, PSI EXPDTA X-RAY DIFFRACTION AUTHOR M.W.VETTING,Y.PATSKOVSKY,R.TORO,J.FREEMAN,S.MILLER,J.M.SAUDER, AUTHOR 2 S.K.BURLEY,D.DUNAWAY-MARIANO,K.N.ALLEN,J.A.GERLT,S.C.ALMO REVDAT 4 20-DEC-23 2YBD 1 REMARK REVDAT 3 03-FEB-21 2YBD 1 AUTHOR JRNL REMARK LINK REVDAT 2 05-JUL-17 2YBD 1 REMARK REVDAT 1 16-MAR-11 2YBD 0 JRNL AUTH M.W.VETTING,Y.PATSKOVSKY,R.TORO,J.FREEMAN,S.MILLER, JRNL AUTH 2 J.M.SAUDER,S.K.BURLEY,D.DUNAWAY-MARIANO,K.N.ALLEN,J.A.GERLT, JRNL AUTH 3 S.C.ALMO JRNL TITL CRYSTAL STRUCTURE OF PROBABLE HAD FAMILY HYDROLASE FROM JRNL TITL 2 PSEUDOMONAS FLUORESCENS PF-5 WITH BOUND PHOSPHATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 21908 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1106 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 32.9935 - 3.9997 0.99 2955 154 0.1754 0.2237 REMARK 3 2 3.9997 - 3.1755 1.00 2740 145 0.1652 0.1902 REMARK 3 3 3.1755 - 2.7743 0.99 2680 142 0.1653 0.2256 REMARK 3 4 2.7743 - 2.5208 0.98 2634 136 0.1657 0.2093 REMARK 3 5 2.5208 - 2.3401 0.97 2570 137 0.1658 0.2159 REMARK 3 6 2.3401 - 2.2022 0.96 2523 135 0.1659 0.2408 REMARK 3 7 2.2022 - 2.0919 0.93 2479 132 0.1697 0.2101 REMARK 3 8 2.0919 - 2.0009 0.85 2221 125 0.2162 0.2813 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 : 0.83 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 37.42 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.960 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.11 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.84790 REMARK 3 B22 (A**2) : 0.84790 REMARK 3 B33 (A**2) : -1.69570 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.008 1591 REMARK 3 ANGLE : 1.032 2180 REMARK 3 CHIRALITY : 0.071 244 REMARK 3 PLANARITY : 0.005 288 REMARK 3 DIHEDRAL : 11.246 582 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 2:23) REMARK 3 ORIGIN FOR THE GROUP (A): 50.4335 6.1734 19.3473 REMARK 3 T TENSOR REMARK 3 T11: 0.1926 T22: -0.0572 REMARK 3 T33: 0.0915 T12: 0.1160 REMARK 3 T13: 0.0008 T23: 0.0444 REMARK 3 L TENSOR REMARK 3 L11: 0.2486 L22: 0.3281 REMARK 3 L33: 0.0230 L12: 0.1412 REMARK 3 L13: -0.0290 L23: -0.0771 REMARK 3 S TENSOR REMARK 3 S11: -0.1763 S12: 0.1446 S13: -0.0196 REMARK 3 S21: -0.0944 S22: 0.1445 S23: 0.0450 REMARK 3 S31: -0.0430 S32: -0.0538 S33: 0.0161 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 24:60) REMARK 3 ORIGIN FOR THE GROUP (A): 65.0061 -7.8637 -2.2223 REMARK 3 T TENSOR REMARK 3 T11: 0.1861 T22: 0.0883 REMARK 3 T33: 0.1218 T12: 0.0172 REMARK 3 T13: -0.0424 T23: -0.0012 REMARK 3 L TENSOR REMARK 3 L11: 0.0946 L22: 0.0391 REMARK 3 L33: 0.1035 L12: -0.0174 REMARK 3 L13: -0.0544 L23: -0.0506 REMARK 3 S TENSOR REMARK 3 S11: -0.1496 S12: -0.0090 S13: 0.0007 REMARK 3 S21: 0.0528 S22: 0.0713 S23: -0.1307 REMARK 3 S31: 0.0574 S32: 0.0793 S33: 0.0150 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 61:85) REMARK 3 ORIGIN FOR THE GROUP (A): 51.7545 -1.9329 16.8401 REMARK 3 T TENSOR REMARK 3 T11: 0.1721 T22: 0.0873 REMARK 3 T33: 0.1114 T12: 0.0252 REMARK 3 T13: 0.0057 T23: 0.0138 REMARK 3 L TENSOR REMARK 3 L11: 0.0809 L22: 0.0229 REMARK 3 L33: 0.1088 L12: -0.0222 REMARK 3 L13: -0.0851 L23: -0.0167 REMARK 3 S TENSOR REMARK 3 S11: -0.1060 S12: -0.0214 S13: -0.0819 REMARK 3 S21: 0.0501 S22: 0.0120 S23: 0.0870 REMARK 3 S31: 0.1381 S32: -0.0945 S33: 0.0088 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 86:96) REMARK 3 ORIGIN FOR THE GROUP (A): 43.1174 8.0443 20.5064 REMARK 3 T TENSOR REMARK 3 T11: 0.1885 T22: 0.1470 REMARK 3 T33: 0.1604 T12: 0.0469 REMARK 3 T13: -0.0098 T23: -0.0165 REMARK 3 L TENSOR REMARK 3 L11: 0.0620 L22: 0.0368 REMARK 3 L33: 0.1984 L12: -0.0061 REMARK 3 L13: 0.0126 L23: 0.0693 REMARK 3 S TENSOR REMARK 3 S11: -0.1554 S12: 0.0708 S13: -0.1445 REMARK 3 S21: 0.0087 S22: -0.0509 S23: 0.0786 REMARK 3 S31: -0.0135 S32: -0.0377 S33: 0.0283 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 97:143) REMARK 3 ORIGIN FOR THE GROUP (A): 39.1704 8.5432 19.5103 REMARK 3 T TENSOR REMARK 3 T11: 0.1830 T22: 0.1019 REMARK 3 T33: 0.1955 T12: 0.0504 REMARK 3 T13: -0.0155 T23: -0.0257 REMARK 3 L TENSOR REMARK 3 L11: 0.1405 L22: 0.0998 REMARK 3 L33: 0.1024 L12: -0.1274 REMARK 3 L13: -0.0328 L23: 0.0498 REMARK 3 S TENSOR REMARK 3 S11: -0.0640 S12: 0.0039 S13: -0.1323 REMARK 3 S21: 0.0947 S22: 0.0068 S23: 0.3439 REMARK 3 S31: -0.0613 S32: -0.3163 S33: 0.0181 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 144:197) REMARK 3 ORIGIN FOR THE GROUP (A): 55.7435 14.1125 18.3558 REMARK 3 T TENSOR REMARK 3 T11: 0.1852 T22: 0.0719 REMARK 3 T33: 0.0880 T12: 0.0498 REMARK 3 T13: 0.0178 T23: 0.0050 REMARK 3 L TENSOR REMARK 3 L11: 0.0898 L22: 0.0143 REMARK 3 L33: 0.0648 L12: 0.0193 REMARK 3 L13: -0.0332 L23: -0.0123 REMARK 3 S TENSOR REMARK 3 S11: -0.0168 S12: -0.0659 S13: -0.0314 REMARK 3 S21: -0.0678 S22: 0.0142 S23: 0.0182 REMARK 3 S31: -0.2079 S32: 0.0285 S33: 0.0048 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: MAGNESIUM IN ACTIVE SITE CHOSEN OVER REMARK 3 WATER DUE TO COORDINATION NUMBER AND GEOMETRY. MOST LIKELY DOES REMARK 3 NOT REPRESENT THE TYPICAL COORDINATION DURING CHEMISTRY. REMARK 3 PHOSPHATE IS ASSUMED TO BE BOUND BY THE ACTIVE SITE POSITION REMARK 3 THAT COORDINATES THE PHOSPHATE OF SUBSTRATE. REMARK 4 REMARK 4 2YBD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-MAR-11. REMARK 100 THE DEPOSITION ID IS D_1290047544. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 5.0 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU-MSC RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22605 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 15.30 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.2 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.30000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.400 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: PDB ENTRY 3M9L REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN (10MM HEPES PH 7.5, 150 MM REMARK 280 NACL, 10% GLYCEROL, 5 MM DTT, 5 MM MGCL);RESERVOUR (2.5 M NA/K REMARK 280 PHOSPHATE, 150 MM NACITRATE, PH 5.0;CRYOPROTECTION (1.8 M NA/K REMARK 280 PHOSPHATE, 100 MM NACITRATE, 18.5% GLYCEROL, 185 MM MGSO4) TWO REMARK 280 MINUTE SOAK. 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 83.46667 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 166.93333 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 125.20000 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 208.66667 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 41.73333 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 83.46667 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 166.93333 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 208.66667 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 125.20000 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 41.73333 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: 4100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -67.6 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 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 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 HOH A2103 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2185 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 MSE A 1 REMARK 465 GLU A 198 REMARK 465 GLY A 199 REMARK 465 HIS A 200 REMARK 465 HIS A 201 REMARK 465 HIS A 202 REMARK 465 HIS A 203 REMARK 465 HIS A 204 REMARK 465 HIS A 205 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 MSE A 13 -82.47 -95.78 REMARK 500 MSE A 13 -82.70 -95.17 REMARK 500 ASP A 174 -152.96 -133.83 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 A2007 DISTANCE = 7.35 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 MG A1198 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 12 OD2 REMARK 620 2 ASP A 14 O 93.0 REMARK 620 3 ASP A 152 OD1 98.5 84.5 REMARK 620 4 PO4 A1199 O1 63.8 78.2 154.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1198 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 1199 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 1200 DBREF 2YBD A 1 197 UNP Q4K5L5 Q4K5L5_PSEF5 1 197 SEQADV 2YBD GLU A 198 UNP Q4K5L5 EXPRESSION TAG SEQADV 2YBD GLY A 199 UNP Q4K5L5 EXPRESSION TAG SEQADV 2YBD HIS A 200 UNP Q4K5L5 EXPRESSION TAG SEQADV 2YBD HIS A 201 UNP Q4K5L5 EXPRESSION TAG SEQADV 2YBD HIS A 202 UNP Q4K5L5 EXPRESSION TAG SEQADV 2YBD HIS A 203 UNP Q4K5L5 EXPRESSION TAG SEQADV 2YBD HIS A 204 UNP Q4K5L5 EXPRESSION TAG SEQADV 2YBD HIS A 205 UNP Q4K5L5 EXPRESSION TAG SEQRES 1 A 205 MSE SER LEU SER GLU ILE LYS HIS TRP VAL PHE ASP MSE SEQRES 2 A 205 ASP GLY THR LEU THR ILE ALA VAL HIS ASP PHE ALA ALA SEQRES 3 A 205 ILE ARG GLU ALA LEU SER ILE PRO ALA GLU ASP ASP ILE SEQRES 4 A 205 LEU THR HIS LEU ALA ALA LEU PRO ALA ASP GLU SER ALA SEQRES 5 A 205 ALA LYS HIS ALA TRP LEU LEU GLU HIS GLU ARG ASP LEU SEQRES 6 A 205 ALA GLN GLY SER ARG PRO ALA PRO GLY ALA VAL GLU LEU SEQRES 7 A 205 VAL ARG GLU LEU ALA GLY ARG GLY TYR ARG LEU GLY ILE SEQRES 8 A 205 LEU THR ARG ASN ALA ARG GLU LEU ALA HIS VAL THR LEU SEQRES 9 A 205 GLU ALA ILE GLY LEU ALA ASP CYS PHE ALA GLU ALA ASP SEQRES 10 A 205 VAL LEU GLY ARG ASP GLU ALA PRO PRO LYS PRO HIS PRO SEQRES 11 A 205 GLY GLY LEU LEU LYS LEU ALA GLU ALA TRP ASP VAL SER SEQRES 12 A 205 PRO SER ARG MSE VAL MSE VAL GLY ASP TYR ARG PHE ASP SEQRES 13 A 205 LEU ASP CYS GLY ARG ALA ALA GLY THR ARG THR VAL LEU SEQRES 14 A 205 VAL ASN LEU PRO ASP ASN PRO TRP PRO GLU LEU THR ASP SEQRES 15 A 205 TRP HIS ALA ARG ASP CYS ALA GLN LEU ARG ASP LEU LEU SEQRES 16 A 205 SER ALA GLU GLY HIS HIS HIS HIS HIS HIS MODRES 2YBD MSE A 13 MET SELENOMETHIONINE MODRES 2YBD MSE A 147 MET SELENOMETHIONINE MODRES 2YBD MSE A 149 MET SELENOMETHIONINE HET MSE A 13 16 HET MSE A 147 8 HET MSE A 149 8 HET MG A1198 1 HET PO4 A1199 5 HET PO4 A1200 5 HETNAM MSE SELENOMETHIONINE HETNAM MG MAGNESIUM ION HETNAM PO4 PHOSPHATE ION FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 MG MG 2+ FORMUL 3 PO4 2(O4 P 3-) FORMUL 5 HOH *229(H2 O) HELIX 1 1 SER A 2 ILE A 6 5 5 HELIX 2 2 ASP A 23 LEU A 31 1 9 HELIX 3 3 ASP A 38 LEU A 46 1 9 HELIX 4 4 PRO A 47 HIS A 61 1 15 HELIX 5 5 HIS A 61 LEU A 65 1 5 HELIX 6 6 GLY A 74 ARG A 85 1 12 HELIX 7 7 ALA A 96 ILE A 107 1 12 HELIX 8 8 LEU A 109 PHE A 113 5 5 HELIX 9 9 ALA A 114 ALA A 116 5 3 HELIX 10 10 PRO A 130 ASP A 141 1 12 HELIX 11 11 SER A 143 SER A 145 5 3 HELIX 12 12 TYR A 153 GLY A 164 1 12 HELIX 13 13 TRP A 177 THR A 181 5 5 HELIX 14 14 ASP A 187 ALA A 197 1 11 SHEET 1 AA 6 VAL A 118 LEU A 119 0 SHEET 2 AA 6 ARG A 88 LEU A 92 1 O ILE A 91 N LEU A 119 SHEET 3 AA 6 HIS A 8 PHE A 11 1 O TRP A 9 N GLY A 90 SHEET 4 AA 6 MSE A 147 GLY A 151 1 O VAL A 148 N VAL A 10 SHEET 5 AA 6 ARG A 166 LEU A 169 1 O ARG A 166 N MSE A 149 SHEET 6 AA 6 TRP A 183 HIS A 184 1 O TRP A 183 N LEU A 169 SHEET 1 AB 2 THR A 18 HIS A 22 0 SHEET 2 AB 2 ALA A 66 PRO A 71 -1 N GLN A 67 O VAL A 21 LINK C ASP A 12 N AMSE A 13 1555 1555 1.33 LINK C ASP A 12 N BMSE A 13 1555 1555 1.33 LINK C AMSE A 13 N ASP A 14 1555 1555 1.33 LINK C BMSE A 13 N ASP A 14 1555 1555 1.33 LINK C ARG A 146 N MSE A 147 1555 1555 1.32 LINK C MSE A 147 N VAL A 148 1555 1555 1.33 LINK C VAL A 148 N MSE A 149 1555 1555 1.33 LINK C MSE A 149 N VAL A 150 1555 1555 1.33 LINK OD2 ASP A 12 MG MG A1198 1555 1555 2.63 LINK O ASP A 14 MG MG A1198 1555 1555 2.62 LINK OD1 ASP A 152 MG MG A1198 1555 1555 2.93 LINK MG MG A1198 O1 PO4 A1199 1555 1555 2.83 CISPEP 1 LYS A 127 PRO A 128 0 8.07 SITE 1 AC1 5 ASP A 12 ASP A 14 HIS A 61 ASP A 152 SITE 2 AC1 5 PO4 A1199 SITE 1 AC2 7 ASP A 12 MSE A 13 ASP A 14 THR A 93 SITE 2 AC2 7 ARG A 94 LYS A 127 MG A1198 SITE 1 AC3 3 HIS A 8 ARG A 146 HOH A2176 CRYST1 65.978 65.978 250.400 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 0.015157 0.008751 0.000000 0.00000 SCALE2 0.000000 0.017501 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003994 0.00000