HEADER HYDROLASE 17-MAR-15 4YTA TITLE BOND LENGTH ANALYSIS OF ASP, GLU AND HIS RESIDUES IN TRYPSIN AT 1.2A TITLE 2 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATIONIC TRYPSIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PEPTIDASE S1 (UNP RESIDUES 24-246); COMPND 5 SYNONYM: BETA-TRYPSIN; COMPND 6 EC: 3.4.21.4 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913 KEYWDS SERINE PROTEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.J.FISHER,J.R.HELLIWELL,M.P.BLAKELEY,M.CIANCI,S.MCSWEENY REVDAT 4 16-OCT-24 4YTA 1 REMARK REVDAT 3 07-FEB-24 4YTA 1 SPRSDE REVDAT 2 20-DEC-17 4YTA 1 JRNL REVDAT 1 27-MAY-15 4YTA 0 SPRSDE 07-FEB-24 4YTA 3UNR JRNL AUTH S.J.FISHER,M.P.BLAKELEY,M.CIANCI,S.MCSWEENEY,J.R.HELLIWELL JRNL TITL PROTONATION-STATE DETERMINATION IN PROTEINS USING JRNL TITL 2 HIGH-RESOLUTION X-RAY CRYSTALLOGRAPHY: EFFECTS OF RESOLUTION JRNL TITL 3 AND COMPLETENESS. JRNL REF ACTA CRYSTALLOGR. D BIOL. V. 68 800 2012 JRNL REF 2 CRYSTALLOGR. JRNL REFN ESSN 1399-0047 JRNL PMID 22751665 JRNL DOI 10.1107/S0907444912012589 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 65730 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.106 REMARK 3 R VALUE (WORKING SET) : 0.105 REMARK 3 FREE R VALUE : 0.121 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 3299 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 33.4625 - 3.4602 0.99 2811 150 0.1487 0.1646 REMARK 3 2 3.4602 - 2.7469 0.97 2635 143 0.1249 0.1360 REMARK 3 3 2.7469 - 2.3998 0.98 2628 136 0.1161 0.1466 REMARK 3 4 2.3998 - 2.1804 0.98 2640 147 0.0989 0.1028 REMARK 3 5 2.1804 - 2.0241 0.99 2620 137 0.0940 0.1021 REMARK 3 6 2.0241 - 1.9048 0.98 2640 120 0.0892 0.1003 REMARK 3 7 1.9048 - 1.8094 0.99 2588 141 0.0884 0.1054 REMARK 3 8 1.8094 - 1.7307 0.98 2592 136 0.0862 0.0987 REMARK 3 9 1.7307 - 1.6640 0.98 2593 140 0.0818 0.0962 REMARK 3 10 1.6640 - 1.6066 0.98 2582 137 0.0845 0.1045 REMARK 3 11 1.6066 - 1.5564 0.98 2535 154 0.0805 0.0998 REMARK 3 12 1.5564 - 1.5119 0.97 2576 145 0.0834 0.1183 REMARK 3 13 1.5119 - 1.4721 0.97 2540 134 0.0867 0.1083 REMARK 3 14 1.4721 - 1.4362 0.97 2548 145 0.0862 0.1113 REMARK 3 15 1.4362 - 1.4035 0.97 2518 133 0.0881 0.1161 REMARK 3 16 1.4035 - 1.3737 0.96 2553 128 0.0904 0.1244 REMARK 3 17 1.3737 - 1.3462 0.96 2506 147 0.0944 0.1193 REMARK 3 18 1.3462 - 1.3208 0.97 2544 134 0.0947 0.1147 REMARK 3 19 1.3208 - 1.2972 0.96 2493 132 0.0968 0.1190 REMARK 3 20 1.2972 - 1.2752 0.95 2516 129 0.0979 0.1233 REMARK 3 21 1.2752 - 1.2546 0.96 2495 139 0.1032 0.1292 REMARK 3 22 1.2546 - 1.2353 0.96 2469 133 0.1097 0.1164 REMARK 3 23 1.2353 - 1.2172 0.95 2502 144 0.1200 0.1423 REMARK 3 24 1.2172 - 1.2000 0.95 2495 115 0.1258 0.1309 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.30 REMARK 3 SHRINKAGE RADIUS : 0.05 REMARK 3 K_SOL : 0.49 REMARK 3 B_SOL : 60.63 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.070 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 8.510 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) : -2.14730 REMARK 3 B22 (A**2) : 0.89830 REMARK 3 B33 (A**2) : 1.24900 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 : 0.011 1984 REMARK 3 ANGLE : 1.559 2735 REMARK 3 CHIRALITY : 0.092 304 REMARK 3 PLANARITY : 0.009 348 REMARK 3 DIHEDRAL : 16.043 755 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 4YTA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000208010. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-OCT-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 65730 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 33.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.14900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: PDB ENTRY 1N6X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG8000, 0.2 M AMMONIUM SULFATE, REMARK 280 0.1 M TRIS-HCL, PH 8.0, VAPOR DIFFUSION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 27.17850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.44950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.03950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.44950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.17850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.03950 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -99.0 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 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 HOH A 488 O HOH A 520 2.01 REMARK 500 O HOH A 481 O HOH A 524 2.04 REMARK 500 O2 GOL A 314 O HOH A 634 2.05 REMARK 500 O HOH A 669 O HOH A 707 2.06 REMARK 500 NZ LYS A 224 O HOH A 401 2.10 REMARK 500 O PRO A 150 O HOH A 402 2.12 REMARK 500 O HOH A 447 O HOH A 452 2.17 REMARK 500 O HOH A 707 O HOH A 715 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 OH TYR A 59 OD2 ASP A 151 4545 1.98 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 71 -81.61 -119.33 REMARK 500 ASN A 115 -124.29 -141.77 REMARK 500 ASP A 151 -54.06 74.05 REMARK 500 SER A 214 -64.73 -120.88 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 A 695 DISTANCE = 6.62 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 CA A 304 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 70 OE1 REMARK 620 2 ASN A 72 O 91.2 REMARK 620 3 VAL A 75 O 165.5 81.2 REMARK 620 4 GLU A 80 OE2 102.5 159.8 88.3 REMARK 620 5 HOH A 579 O 86.8 88.9 105.2 77.3 REMARK 620 6 HOH A 599 O 79.7 103.0 90.0 94.1 162.1 REMARK 620 N 1 2 3 4 5 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 310 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 311 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BEN A 312 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 313 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 314 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3UNR RELATED DB: PDB REMARK 900 PROTONATION STATE ANALYSIS FOR THIS STRUCTURE WAS CONDUCTED USING REMARK 900 SHELX, HOWEVER SUBMISSION OF SHELX PDB FILES WITH HYDROGEN ATOMS TO REMARK 900 THE PDB IS NOT CURRENTLY POSSIBLE DUE TO SHELX USING A NON STANDARD REMARK 900 NAMING CONVENTION. AS SUCH THE PRIOR MODEL FROM PHENIX WAS REMARK 900 SUBMITTED. READY_SET! FROM THE PHENIX SUITE WAS USED TO GENERATE REMARK 900 THE MODEL WITH THE H-ATOMS INCLUDED. IN THE VERSION OF READY_SET! REMARK 900 USED AT THE TIME THE DEFAULT SETTING GENERATED DOUBLY PROTONATED REMARK 900 (I.E. CHARGED) HISTIDINES AND IT WAS THE TASK OF THE USER TO REMARK 900 CAREFULLY DELETE THOSE H-ATOMS WHICH ARE NOT ACTUALLY PRESENT. A REMARK 900 SIMPLE OVERSIGHT OF NOT DELETING ONE OF THESE H-ATOMS ATTACHED TO A REMARK 900 HISTIDINE LED TO THE SUBMISSION OF AN INCORRECT MODEL IN THAT REMARK 900 DETAIL. THIS WAS IDENTIFIED BY Z DAUTER ET AL (2013) AND WE THANK REMARK 900 THEM FOR NOTICING THIS ERROR AND HAVE CONSEQUENTLY UPLOADED A REMARK 900 CORRECTED PDB MODEL WITH THIS H-ATOM OMITTED. HTTP:// REMARK 900 JOURNALS.IUCR.ORG/M/ISSUES/2014/03/00/DC5002/INDEX.HTML DBREF 4YTA A 16 245 UNP P00760 TRY1_BOVIN 24 246 SEQRES 1 A 223 ILE VAL GLY GLY TYR THR CYS GLY ALA ASN THR VAL PRO SEQRES 2 A 223 TYR GLN VAL SER LEU ASN SER GLY TYR HIS PHE CYS GLY SEQRES 3 A 223 GLY SER LEU ILE ASN SER GLN TRP VAL VAL SER ALA ALA SEQRES 4 A 223 HIS CYS TYR LYS SER GLY ILE GLN VAL ARG LEU GLY GLU SEQRES 5 A 223 ASP ASN ILE ASN VAL VAL GLU GLY ASN GLU GLN PHE ILE SEQRES 6 A 223 SER ALA SER LYS SER ILE VAL HIS PRO SER TYR ASN SER SEQRES 7 A 223 ASN THR LEU ASN ASN ASP ILE MET LEU ILE LYS LEU LYS SEQRES 8 A 223 SER ALA ALA SER LEU ASN SER ARG VAL ALA SER ILE SER SEQRES 9 A 223 LEU PRO THR SER CYS ALA SER ALA GLY THR GLN CYS LEU SEQRES 10 A 223 ILE SER GLY TRP GLY ASN THR LYS SER SER GLY THR SER SEQRES 11 A 223 TYR PRO ASP VAL LEU LYS CYS LEU LYS ALA PRO ILE LEU SEQRES 12 A 223 SER ASP SER SER CYS LYS SER ALA TYR PRO GLY GLN ILE SEQRES 13 A 223 THR SER ASN MET PHE CYS ALA GLY TYR LEU GLU GLY GLY SEQRES 14 A 223 LYS ASP SER CYS GLN GLY ASP SER GLY GLY PRO VAL VAL SEQRES 15 A 223 CYS SER GLY LYS LEU GLN GLY ILE VAL SER TRP GLY SER SEQRES 16 A 223 GLY CYS ALA GLN LYS ASN LYS PRO GLY VAL TYR THR LYS SEQRES 17 A 223 VAL CYS ASN TYR VAL SER TRP ILE LYS GLN THR ILE ALA SEQRES 18 A 223 SER ASN HET GOL A 301 14 HET GOL A 302 14 HET SO4 A 303 5 HET CA A 304 1 HET SO4 A 305 5 HET SO4 A 306 5 HET SO4 A 307 5 HET SO4 A 308 5 HET SO4 A 309 5 HET SO4 A 310 5 HET SO4 A 311 5 HET BEN A 312 16 HET GOL A 313 14 HET GOL A 314 14 HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETNAM CA CALCIUM ION HETNAM BEN BENZAMIDINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 4(C3 H8 O3) FORMUL 4 SO4 8(O4 S 2-) FORMUL 5 CA CA 2+ FORMUL 13 BEN C7 H8 N2 FORMUL 16 HOH *337(H2 O) HELIX 1 AA1 ALA A 55 TYR A 59 5 5 HELIX 2 AA2 SER A 162 TYR A 170 1 9 HELIX 3 AA3 TYR A 234 ASN A 245 1 12 SHEET 1 AA1 7 TYR A 20 THR A 21 0 SHEET 2 AA1 7 LYS A 154 PRO A 159 -1 O CYS A 155 N TYR A 20 SHEET 3 AA1 7 GLN A 133 GLY A 138 -1 N ILE A 136 O LEU A 156 SHEET 4 AA1 7 PRO A 198 CYS A 201 -1 O VAL A 200 N LEU A 135 SHEET 5 AA1 7 LYS A 204 TRP A 215 -1 O LYS A 204 N CYS A 201 SHEET 6 AA1 7 GLY A 226 LYS A 230 -1 O VAL A 227 N TRP A 215 SHEET 7 AA1 7 MET A 178 ALA A 181 -1 N PHE A 179 O TYR A 228 SHEET 1 AA2 7 GLN A 30 ASN A 34 0 SHEET 2 AA2 7 HIS A 40 ASN A 48 -1 O CYS A 42 N LEU A 33 SHEET 3 AA2 7 TRP A 51 SER A 54 -1 O VAL A 53 N SER A 45 SHEET 4 AA2 7 MET A 104 LEU A 108 -1 O ILE A 106 N VAL A 52 SHEET 5 AA2 7 GLN A 81 VAL A 90 -1 N ILE A 89 O LEU A 105 SHEET 6 AA2 7 GLN A 64 LEU A 67 -1 N LEU A 67 O GLN A 81 SHEET 7 AA2 7 GLN A 30 ASN A 34 -1 N SER A 32 O ARG A 66 SSBOND 1 CYS A 22 CYS A 155 1555 1555 2.04 SSBOND 2 CYS A 42 CYS A 58 1555 1555 2.06 SSBOND 3 CYS A 127 CYS A 232 1555 1555 2.03 SSBOND 4 CYS A 134 CYS A 201 1555 1555 2.02 SSBOND 5 CYS A 166 CYS A 180 1555 1555 2.05 SSBOND 6 CYS A 191 CYS A 219 1555 1555 2.08 LINK OE1 GLU A 70 CA CA A 304 1555 1555 2.27 LINK O ASN A 72 CA CA A 304 1555 1555 2.35 LINK O VAL A 75 CA CA A 304 1555 1555 2.30 LINK OE2 GLU A 80 CA CA A 304 1555 1555 2.32 LINK CA CA A 304 O HOH A 579 1555 1555 2.40 LINK CA CA A 304 O HOH A 599 1555 1555 2.35 SITE 1 AC1 11 ASN A 97 THR A 98 LEU A 99 LYS A 157 SITE 2 AC1 11 GLN A 173 TRP A 215 GOL A 302 HOH A 406 SITE 3 AC1 11 HOH A 422 HOH A 425 HOH A 428 SITE 1 AC2 10 TYR A 20 CYS A 22 THR A 26 ASN A 97 SITE 2 AC2 10 LEU A 135 GLN A 173 GOL A 301 HOH A 406 SITE 3 AC2 10 HOH A 428 HOH A 447 SITE 1 AC3 2 ILE A 47 ASN A 48 SITE 1 AC4 6 GLU A 70 ASN A 72 VAL A 75 GLU A 80 SITE 2 AC4 6 HOH A 579 HOH A 599 SITE 1 AC5 9 PRO A 124 THR A 125 SER A 126 SER A 145 SITE 2 AC5 9 GLY A 146 LYS A 204 HOH A 456 HOH A 467 SITE 3 AC5 9 HOH A 489 SITE 1 AC6 8 HIS A 57 GLN A 192 GLY A 193 SER A 195 SITE 2 AC6 8 BEN A 312 HOH A 448 HOH A 596 HOH A 647 SITE 1 AC7 9 LYS A 87 LYS A 107 THR A 147 TYR A 149 SITE 2 AC7 9 HOH A 426 HOH A 450 HOH A 451 HOH A 477 SITE 3 AC7 9 HOH A 502 SITE 1 AC8 6 LYS A 143 SER A 144 SER A 145 HOH A 696 SITE 2 AC8 6 HOH A 713 HOH A 718 SITE 1 AC9 4 THR A 175 SER A 176 HOH A 620 HOH A 683 SITE 1 AD1 7 LYS A 167 PRO A 171 GLY A 172 HOH A 446 SITE 2 AD1 7 HOH A 533 HOH A 593 HOH A 692 SITE 1 AD2 7 ASN A 95 THR A 98 ASN A 100 HOH A 629 SITE 2 AD2 7 HOH A 649 HOH A 650 HOH A 676 SITE 1 AD3 9 ASP A 189 SER A 190 GLN A 192 SER A 195 SITE 2 AD3 9 GLY A 218 CYS A 219 GLY A 226 SO4 A 306 SITE 3 AD3 9 HOH A 584 SITE 1 AD4 4 GLU A 80 GLN A 81 PHE A 82 HOH A 539 SITE 1 AD5 9 THR A 142 PRO A 150 LYS A 154 HOH A 585 SITE 2 AD5 9 HOH A 611 HOH A 617 HOH A 634 HOH A 693 SITE 3 AD5 9 HOH A 731 CRYST1 54.357 58.079 66.899 90.00 90.00 90.00 P 21 21 21 4 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 0.018397 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017218 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014948 0.00000