HEADER HYDROLASE 08-SEP-15 5DM5 TITLE CRYSTAL STRUCTURE OF THE HEXAMERIC THIOESTERASE Y2039 FROM YERSINIA TITLE 2 PESTIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE ACYL-COA THIOESTER HYDROLASE; COMPND 3 CHAIN: A, B, C, D, E, F; COMPND 4 EC: 3.1.2.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YERSINIA PESTIS KIM10+; SOURCE 3 ORGANISM_TAXID: 632; SOURCE 4 STRAIN: KIM10+; SOURCE 5 GENE: Y2039, YPO2195; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS THIOESTERASE, HOT-DOG FOLD, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.M.D.SWARBRICK,J.K.FORWOOD REVDAT 3 27-SEP-23 5DM5 1 REMARK REVDAT 2 23-AUG-17 5DM5 1 REMARK REVDAT 1 11-NOV-15 5DM5 0 JRNL AUTH C.M.D.SWARBRICK,J.K.FORWOOD JRNL TITL CRYSTAL STRUCTURE OF THE HEXAMERIC THIOESTERASE Y2039 FROM JRNL TITL 2 YERSINIA PESTIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10PRE_2104: ???) 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 : TWIN_LSQ_F REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 25310 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1281 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 19.2891 - 5.5764 0.85 2514 138 0.1881 0.2274 REMARK 3 2 5.5764 - 4.4440 0.89 2662 149 0.1686 0.2449 REMARK 3 3 4.4440 - 3.8874 0.90 2628 120 0.1886 0.2402 REMARK 3 4 3.8874 - 3.5344 0.90 2686 131 0.2450 0.2446 REMARK 3 5 3.5344 - 3.2824 0.91 2699 143 0.2694 0.3051 REMARK 3 6 3.2824 - 3.0897 0.91 2702 148 0.2891 0.2671 REMARK 3 7 3.0897 - 2.9355 0.91 2689 159 0.3181 0.3559 REMARK 3 8 2.9355 - 2.8081 0.92 2710 130 0.3271 0.2964 REMARK 3 9 2.8081 - 2.7003 0.91 2689 150 0.3489 0.3752 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) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.510 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 : 0.012 5569 REMARK 3 ANGLE : 1.675 7527 REMARK 3 CHIRALITY : 0.262 876 REMARK 3 PLANARITY : 0.009 958 REMARK 3 DIHEDRAL : 13.337 2028 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 5DM5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000213425. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-AUG-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25310 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 34.878 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.14500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.0000 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) : 2.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.63800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 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: 1YLI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 800 MM POTASSIUM SODIUM TARTRATE REMARK 280 TETRAHYDRATE, 120 MM HEPES, PH 7.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 296.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 190.17333 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 95.08667 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 142.63000 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 47.54333 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 237.71667 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A -2 REMARK 465 ASN A -1 REMARK 465 ALA A 0 REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 GLN A 3 REMARK 465 GLU A 4 REMARK 465 GLN A 5 REMARK 465 GLN A 6 REMARK 465 LEU A 7 REMARK 465 SER A 8 REMARK 465 GLY A 9 REMARK 465 GLY A 10 REMARK 465 GLU A 11 REMARK 465 LEU A 12 REMARK 465 VAL A 106 REMARK 465 SER A 107 REMARK 465 SER A 108 REMARK 465 PRO A 133 REMARK 465 ARG A 134 REMARK 465 GLY A 135 REMARK 465 LEU A 136 REMARK 465 PRO A 137 REMARK 465 SER A 138 REMARK 465 GLY A 139 REMARK 465 LYS A 140 REMARK 465 GLY A 141 REMARK 465 ASN A 142 REMARK 465 PHE A 143 REMARK 465 GLU A 144 REMARK 465 VAL A 145 REMARK 465 GLY A 146 REMARK 465 ALA A 147 REMARK 465 THR A 148 REMARK 465 GLN A 149 REMARK 465 SER B -2 REMARK 465 ASN B -1 REMARK 465 ALA B 0 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 GLN B 3 REMARK 465 GLU B 4 REMARK 465 GLN B 5 REMARK 465 GLN B 6 REMARK 465 LEU B 7 REMARK 465 SER B 8 REMARK 465 GLY B 9 REMARK 465 GLY B 10 REMARK 465 GLU B 11 REMARK 465 LEU B 12 REMARK 465 SER B 13 REMARK 465 GLY B 139 REMARK 465 LYS B 140 REMARK 465 GLY B 141 REMARK 465 ASN B 142 REMARK 465 PHE B 143 REMARK 465 GLU B 144 REMARK 465 VAL B 145 REMARK 465 GLY B 146 REMARK 465 ALA B 147 REMARK 465 THR B 148 REMARK 465 GLN B 149 REMARK 465 SER C -2 REMARK 465 ASN C -1 REMARK 465 ALA C 0 REMARK 465 MET C 1 REMARK 465 THR C 2 REMARK 465 GLN C 3 REMARK 465 GLU C 4 REMARK 465 GLN C 5 REMARK 465 GLN C 6 REMARK 465 LEU C 7 REMARK 465 SER C 8 REMARK 465 GLY C 9 REMARK 465 GLY C 10 REMARK 465 GLU C 11 REMARK 465 LEU C 12 REMARK 465 SER C 13 REMARK 465 SER C 108 REMARK 465 GLU C 109 REMARK 465 PRO C 110 REMARK 465 ILE C 111 REMARK 465 GLY C 112 REMARK 465 LYS C 140 REMARK 465 GLY C 141 REMARK 465 ASN C 142 REMARK 465 PHE C 143 REMARK 465 GLU C 144 REMARK 465 VAL C 145 REMARK 465 GLY C 146 REMARK 465 ALA C 147 REMARK 465 THR C 148 REMARK 465 GLN C 149 REMARK 465 SER D -2 REMARK 465 ASN D -1 REMARK 465 ALA D 0 REMARK 465 MET D 1 REMARK 465 THR D 2 REMARK 465 GLN D 3 REMARK 465 GLU D 4 REMARK 465 GLN D 5 REMARK 465 GLN D 6 REMARK 465 LEU D 7 REMARK 465 SER D 8 REMARK 465 GLY D 9 REMARK 465 GLY D 10 REMARK 465 GLU D 11 REMARK 465 LEU D 12 REMARK 465 SER D 108 REMARK 465 GLU D 109 REMARK 465 PRO D 110 REMARK 465 ILE D 111 REMARK 465 GLY D 112 REMARK 465 GLY D 139 REMARK 465 LYS D 140 REMARK 465 GLY D 141 REMARK 465 ASN D 142 REMARK 465 PHE D 143 REMARK 465 GLU D 144 REMARK 465 VAL D 145 REMARK 465 GLY D 146 REMARK 465 ALA D 147 REMARK 465 THR D 148 REMARK 465 GLN D 149 REMARK 465 SER E -2 REMARK 465 ASN E -1 REMARK 465 ALA E 0 REMARK 465 MET E 1 REMARK 465 THR E 2 REMARK 465 GLN E 3 REMARK 465 GLU E 4 REMARK 465 GLN E 5 REMARK 465 GLN E 6 REMARK 465 LEU E 7 REMARK 465 SER E 8 REMARK 465 GLY E 9 REMARK 465 GLY E 10 REMARK 465 GLU E 11 REMARK 465 LEU E 12 REMARK 465 SER E 13 REMARK 465 VAL E 106 REMARK 465 SER E 107 REMARK 465 SER E 108 REMARK 465 GLU E 109 REMARK 465 PRO E 110 REMARK 465 ILE E 111 REMARK 465 GLY E 112 REMARK 465 LYS E 140 REMARK 465 GLY E 141 REMARK 465 ASN E 142 REMARK 465 PHE E 143 REMARK 465 GLU E 144 REMARK 465 VAL E 145 REMARK 465 GLY E 146 REMARK 465 ALA E 147 REMARK 465 THR E 148 REMARK 465 GLN E 149 REMARK 465 SER F -2 REMARK 465 ASN F -1 REMARK 465 ALA F 0 REMARK 465 MET F 1 REMARK 465 THR F 2 REMARK 465 GLN F 3 REMARK 465 GLU F 4 REMARK 465 GLN F 5 REMARK 465 GLN F 6 REMARK 465 LEU F 7 REMARK 465 SER F 8 REMARK 465 GLY F 9 REMARK 465 GLY F 10 REMARK 465 GLU F 11 REMARK 465 LEU F 12 REMARK 465 SER F 13 REMARK 465 SER F 108 REMARK 465 GLU F 109 REMARK 465 PRO F 110 REMARK 465 ILE F 111 REMARK 465 LYS F 140 REMARK 465 GLY F 141 REMARK 465 ASN F 142 REMARK 465 PHE F 143 REMARK 465 GLU F 144 REMARK 465 VAL F 145 REMARK 465 GLY F 146 REMARK 465 ALA F 147 REMARK 465 THR F 148 REMARK 465 GLN F 149 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 OE2 GLU C 55 NZ LYS F 104 1.76 REMARK 500 OD1 ASP A 46 O GLY B 38 2.03 REMARK 500 ND2 ASN B 31 O ASP B 35 2.04 REMARK 500 NH2 ARG F 65 OD1 ASP F 67 2.16 REMARK 500 NZ LYS A 104 OE2 GLU D 55 2.18 REMARK 500 OD1 ASP B 79 N SER B 107 2.19 REMARK 500 ND2 ASN B 98 OE2 GLU B 119 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 LEU B 14 NH1 ARG C 65 5655 2.11 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 PRO A 110 C - N - CD ANGL. DEV. = 13.1 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 ASP A 29 31.24 -98.63 REMARK 500 ASN A 31 -164.17 -107.80 REMARK 500 ALA B 28 -7.30 85.38 REMARK 500 ASN B 31 -166.98 -108.97 REMARK 500 SER B 107 -139.09 59.96 REMARK 500 ASN C 31 -168.91 -107.15 REMARK 500 THR C 90 75.62 -117.34 REMARK 500 PRO C 137 -174.11 -64.85 REMARK 500 ASN D 31 -164.57 -111.33 REMARK 500 ASN E 31 -169.24 -103.23 REMARK 500 PRO F 15 98.58 -67.09 REMARK 500 ASN F 31 -161.77 -108.57 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 C 38 GLY C 39 141.77 REMARK 500 SER C 138 GLY C 139 -147.94 REMARK 500 GLY D 38 GLY D 39 144.74 REMARK 500 GLY E 38 GLY E 39 145.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 SER C 138 12.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE D 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL E 201 DBREF 5DM5 A 1 149 UNP Q7CIM6 Q7CIM6_YERPE 1 149 DBREF 5DM5 B 1 149 UNP Q7CIM6 Q7CIM6_YERPE 1 149 DBREF 5DM5 C 1 149 UNP Q7CIM6 Q7CIM6_YERPE 1 149 DBREF 5DM5 D 1 149 UNP Q7CIM6 Q7CIM6_YERPE 1 149 DBREF 5DM5 E 1 149 UNP Q7CIM6 Q7CIM6_YERPE 1 149 DBREF 5DM5 F 1 149 UNP Q7CIM6 Q7CIM6_YERPE 1 149 SEQADV 5DM5 SER A -2 UNP Q7CIM6 EXPRESSION TAG SEQADV 5DM5 ASN A -1 UNP Q7CIM6 EXPRESSION TAG SEQADV 5DM5 ALA A 0 UNP Q7CIM6 EXPRESSION TAG SEQADV 5DM5 SER B -2 UNP Q7CIM6 EXPRESSION TAG SEQADV 5DM5 ASN B -1 UNP Q7CIM6 EXPRESSION TAG SEQADV 5DM5 ALA B 0 UNP Q7CIM6 EXPRESSION TAG SEQADV 5DM5 SER C -2 UNP Q7CIM6 EXPRESSION TAG SEQADV 5DM5 ASN C -1 UNP Q7CIM6 EXPRESSION TAG SEQADV 5DM5 ALA C 0 UNP Q7CIM6 EXPRESSION TAG SEQADV 5DM5 SER D -2 UNP Q7CIM6 EXPRESSION TAG SEQADV 5DM5 ASN D -1 UNP Q7CIM6 EXPRESSION TAG SEQADV 5DM5 ALA D 0 UNP Q7CIM6 EXPRESSION TAG SEQADV 5DM5 SER E -2 UNP Q7CIM6 EXPRESSION TAG SEQADV 5DM5 ASN E -1 UNP Q7CIM6 EXPRESSION TAG SEQADV 5DM5 ALA E 0 UNP Q7CIM6 EXPRESSION TAG SEQADV 5DM5 SER F -2 UNP Q7CIM6 EXPRESSION TAG SEQADV 5DM5 ASN F -1 UNP Q7CIM6 EXPRESSION TAG SEQADV 5DM5 ALA F 0 UNP Q7CIM6 EXPRESSION TAG SEQRES 1 A 152 SER ASN ALA MET THR GLN GLU GLN GLN LEU SER GLY GLY SEQRES 2 A 152 GLU LEU SER LEU PRO ASN GLY GLU LEU VAL LEU ARG THR SEQRES 3 A 152 LEU ALA MET PRO ALA ASP THR ASN ALA ASN GLY ASP ILE SEQRES 4 A 152 PHE GLY GLY TRP LEU MET SER GLN MET ASP ILE GLY GLY SEQRES 5 A 152 ALA ILE GLN ALA LYS GLU ILE ALA GLN GLY ARG VAL VAL SEQRES 6 A 152 THR VAL ARG VAL ASP GLY MET THR PHE LEU LYS PRO VAL SEQRES 7 A 152 ALA VAL GLY ASP VAL VAL CYS CYS TYR ALA ARG CYS ILE SEQRES 8 A 152 LYS THR GLY HIS SER SER ILE THR ILE ASN ILE GLU VAL SEQRES 9 A 152 TRP VAL LYS LYS VAL SER SER GLU PRO ILE GLY GLN ARG SEQRES 10 A 152 TYR ARG ALA THR GLU ALA VAL PHE THR TYR VAL ALA VAL SEQRES 11 A 152 ASP ASP ALA GLY LYS PRO ARG GLY LEU PRO SER GLY LYS SEQRES 12 A 152 GLY ASN PHE GLU VAL GLY ALA THR GLN SEQRES 1 B 152 SER ASN ALA MET THR GLN GLU GLN GLN LEU SER GLY GLY SEQRES 2 B 152 GLU LEU SER LEU PRO ASN GLY GLU LEU VAL LEU ARG THR SEQRES 3 B 152 LEU ALA MET PRO ALA ASP THR ASN ALA ASN GLY ASP ILE SEQRES 4 B 152 PHE GLY GLY TRP LEU MET SER GLN MET ASP ILE GLY GLY SEQRES 5 B 152 ALA ILE GLN ALA LYS GLU ILE ALA GLN GLY ARG VAL VAL SEQRES 6 B 152 THR VAL ARG VAL ASP GLY MET THR PHE LEU LYS PRO VAL SEQRES 7 B 152 ALA VAL GLY ASP VAL VAL CYS CYS TYR ALA ARG CYS ILE SEQRES 8 B 152 LYS THR GLY HIS SER SER ILE THR ILE ASN ILE GLU VAL SEQRES 9 B 152 TRP VAL LYS LYS VAL SER SER GLU PRO ILE GLY GLN ARG SEQRES 10 B 152 TYR ARG ALA THR GLU ALA VAL PHE THR TYR VAL ALA VAL SEQRES 11 B 152 ASP ASP ALA GLY LYS PRO ARG GLY LEU PRO SER GLY LYS SEQRES 12 B 152 GLY ASN PHE GLU VAL GLY ALA THR GLN SEQRES 1 C 152 SER ASN ALA MET THR GLN GLU GLN GLN LEU SER GLY GLY SEQRES 2 C 152 GLU LEU SER LEU PRO ASN GLY GLU LEU VAL LEU ARG THR SEQRES 3 C 152 LEU ALA MET PRO ALA ASP THR ASN ALA ASN GLY ASP ILE SEQRES 4 C 152 PHE GLY GLY TRP LEU MET SER GLN MET ASP ILE GLY GLY SEQRES 5 C 152 ALA ILE GLN ALA LYS GLU ILE ALA GLN GLY ARG VAL VAL SEQRES 6 C 152 THR VAL ARG VAL ASP GLY MET THR PHE LEU LYS PRO VAL SEQRES 7 C 152 ALA VAL GLY ASP VAL VAL CYS CYS TYR ALA ARG CYS ILE SEQRES 8 C 152 LYS THR GLY HIS SER SER ILE THR ILE ASN ILE GLU VAL SEQRES 9 C 152 TRP VAL LYS LYS VAL SER SER GLU PRO ILE GLY GLN ARG SEQRES 10 C 152 TYR ARG ALA THR GLU ALA VAL PHE THR TYR VAL ALA VAL SEQRES 11 C 152 ASP ASP ALA GLY LYS PRO ARG GLY LEU PRO SER GLY LYS SEQRES 12 C 152 GLY ASN PHE GLU VAL GLY ALA THR GLN SEQRES 1 D 152 SER ASN ALA MET THR GLN GLU GLN GLN LEU SER GLY GLY SEQRES 2 D 152 GLU LEU SER LEU PRO ASN GLY GLU LEU VAL LEU ARG THR SEQRES 3 D 152 LEU ALA MET PRO ALA ASP THR ASN ALA ASN GLY ASP ILE SEQRES 4 D 152 PHE GLY GLY TRP LEU MET SER GLN MET ASP ILE GLY GLY SEQRES 5 D 152 ALA ILE GLN ALA LYS GLU ILE ALA GLN GLY ARG VAL VAL SEQRES 6 D 152 THR VAL ARG VAL ASP GLY MET THR PHE LEU LYS PRO VAL SEQRES 7 D 152 ALA VAL GLY ASP VAL VAL CYS CYS TYR ALA ARG CYS ILE SEQRES 8 D 152 LYS THR GLY HIS SER SER ILE THR ILE ASN ILE GLU VAL SEQRES 9 D 152 TRP VAL LYS LYS VAL SER SER GLU PRO ILE GLY GLN ARG SEQRES 10 D 152 TYR ARG ALA THR GLU ALA VAL PHE THR TYR VAL ALA VAL SEQRES 11 D 152 ASP ASP ALA GLY LYS PRO ARG GLY LEU PRO SER GLY LYS SEQRES 12 D 152 GLY ASN PHE GLU VAL GLY ALA THR GLN SEQRES 1 E 152 SER ASN ALA MET THR GLN GLU GLN GLN LEU SER GLY GLY SEQRES 2 E 152 GLU LEU SER LEU PRO ASN GLY GLU LEU VAL LEU ARG THR SEQRES 3 E 152 LEU ALA MET PRO ALA ASP THR ASN ALA ASN GLY ASP ILE SEQRES 4 E 152 PHE GLY GLY TRP LEU MET SER GLN MET ASP ILE GLY GLY SEQRES 5 E 152 ALA ILE GLN ALA LYS GLU ILE ALA GLN GLY ARG VAL VAL SEQRES 6 E 152 THR VAL ARG VAL ASP GLY MET THR PHE LEU LYS PRO VAL SEQRES 7 E 152 ALA VAL GLY ASP VAL VAL CYS CYS TYR ALA ARG CYS ILE SEQRES 8 E 152 LYS THR GLY HIS SER SER ILE THR ILE ASN ILE GLU VAL SEQRES 9 E 152 TRP VAL LYS LYS VAL SER SER GLU PRO ILE GLY GLN ARG SEQRES 10 E 152 TYR ARG ALA THR GLU ALA VAL PHE THR TYR VAL ALA VAL SEQRES 11 E 152 ASP ASP ALA GLY LYS PRO ARG GLY LEU PRO SER GLY LYS SEQRES 12 E 152 GLY ASN PHE GLU VAL GLY ALA THR GLN SEQRES 1 F 152 SER ASN ALA MET THR GLN GLU GLN GLN LEU SER GLY GLY SEQRES 2 F 152 GLU LEU SER LEU PRO ASN GLY GLU LEU VAL LEU ARG THR SEQRES 3 F 152 LEU ALA MET PRO ALA ASP THR ASN ALA ASN GLY ASP ILE SEQRES 4 F 152 PHE GLY GLY TRP LEU MET SER GLN MET ASP ILE GLY GLY SEQRES 5 F 152 ALA ILE GLN ALA LYS GLU ILE ALA GLN GLY ARG VAL VAL SEQRES 6 F 152 THR VAL ARG VAL ASP GLY MET THR PHE LEU LYS PRO VAL SEQRES 7 F 152 ALA VAL GLY ASP VAL VAL CYS CYS TYR ALA ARG CYS ILE SEQRES 8 F 152 LYS THR GLY HIS SER SER ILE THR ILE ASN ILE GLU VAL SEQRES 9 F 152 TRP VAL LYS LYS VAL SER SER GLU PRO ILE GLY GLN ARG SEQRES 10 F 152 TYR ARG ALA THR GLU ALA VAL PHE THR TYR VAL ALA VAL SEQRES 11 F 152 ASP ASP ALA GLY LYS PRO ARG GLY LEU PRO SER GLY LYS SEQRES 12 F 152 GLY ASN PHE GLU VAL GLY ALA THR GLN HET GOL A 201 6 HET PGE B 201 10 HET PGE C 201 10 HET PGE D 201 10 HET GOL E 201 6 HETNAM GOL GLYCEROL HETNAM PGE TRIETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 7 GOL 2(C3 H8 O3) FORMUL 8 PGE 3(C6 H14 O4) HELIX 1 AA1 MET A 26 THR A 30 5 5 HELIX 2 AA2 PHE A 37 GLN A 58 1 22 HELIX 3 AA3 GLY B 39 GLN B 58 1 20 HELIX 4 AA4 MET C 26 THR C 30 5 5 HELIX 5 AA5 PHE C 37 GLN C 58 1 22 HELIX 6 AA6 MET D 26 THR D 30 5 5 HELIX 7 AA7 PHE D 37 GLN D 58 1 22 HELIX 8 AA8 MET E 26 THR E 30 5 5 HELIX 9 AA9 PHE E 37 GLN E 58 1 22 HELIX 10 AB1 MET F 26 THR F 30 5 5 HELIX 11 AB2 GLY F 39 ALA F 57 1 19 SHEET 1 AA110 GLU A 18 LEU A 24 0 SHEET 2 AA110 VAL A 80 LYS A 89 -1 O CYS A 83 N VAL A 20 SHEET 3 AA110 SER A 94 VAL A 103 -1 O TRP A 102 N CYS A 82 SHEET 4 AA110 TYR A 115 ALA A 126 -1 O ALA A 117 N VAL A 101 SHEET 5 AA110 VAL A 61 PHE A 71 -1 N THR A 70 O GLU A 119 SHEET 6 AA110 VAL B 61 PHE B 71 -1 O PHE B 71 N VAL A 64 SHEET 7 AA110 TYR B 115 ALA B 126 -1 O THR B 123 N VAL B 64 SHEET 8 AA110 SER B 94 VAL B 103 -1 N VAL B 101 O ALA B 117 SHEET 9 AA110 VAL B 80 THR B 90 -1 N CYS B 82 O TRP B 102 SHEET 10 AA110 GLU B 18 LEU B 24 -1 N LEU B 21 O CYS B 83 SHEET 1 AA210 GLU C 18 LEU C 24 0 SHEET 2 AA210 VAL C 80 THR C 90 -1 O VAL C 81 N THR C 23 SHEET 3 AA210 SER C 94 LYS C 104 -1 O THR C 96 N LYS C 89 SHEET 4 AA210 TYR C 115 ALA C 126 -1 O PHE C 122 N ILE C 97 SHEET 5 AA210 VAL C 61 PHE C 71 -1 N VAL C 64 O THR C 123 SHEET 6 AA210 ARG D 60 THR D 70 -1 O MET D 69 N VAL C 66 SHEET 7 AA210 TYR D 115 VAL D 127 -1 O THR D 123 N ARG D 65 SHEET 8 AA210 SER D 94 VAL D 103 -1 N VAL D 101 O ALA D 117 SHEET 9 AA210 VAL D 80 THR D 90 -1 N CYS D 82 O TRP D 102 SHEET 10 AA210 GLU D 18 LEU D 24 -1 N LEU D 21 O CYS D 83 SHEET 1 AA310 GLU E 18 LEU E 24 0 SHEET 2 AA310 VAL E 80 THR E 90 -1 O VAL E 81 N THR E 23 SHEET 3 AA310 SER E 94 LYS E 104 -1 O GLU E 100 N TYR E 84 SHEET 4 AA310 TYR E 115 ALA E 126 -1 O TYR E 115 N VAL E 103 SHEET 5 AA310 VAL E 61 PHE E 71 -1 N THR E 70 O GLU E 119 SHEET 6 AA310 VAL F 61 PHE F 71 -1 O VAL F 64 N PHE E 71 SHEET 7 AA310 TYR F 115 ALA F 126 -1 O GLU F 119 N THR F 70 SHEET 8 AA310 SER F 94 VAL F 103 -1 N VAL F 101 O ALA F 117 SHEET 9 AA310 VAL F 80 THR F 90 -1 N TYR F 84 O GLU F 100 SHEET 10 AA310 GLU F 18 LEU F 24 -1 N THR F 23 O VAL F 81 SITE 1 AC1 3 THR A 90 GLY A 91 HIS A 92 SITE 1 AC2 4 ILE B 88 THR B 90 GLY B 91 SER B 138 SITE 1 AC3 3 ILE C 88 THR C 90 PRO E 15 SITE 1 AC4 1 ILE D 88 SITE 1 AC5 2 ILE E 88 THR E 90 CRYST1 77.870 77.870 285.260 90.00 90.00 120.00 P 65 36 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 0.012842 0.007414 0.000000 0.00000 SCALE2 0.000000 0.014829 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003506 0.00000