HEADER PENICILLIN-BINDING PROTEIN 10-JAN-23 8C5W TITLE CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 (PBP3) FROM TITLE 2 STAPHYLOCOCCUS EPIDERMIDIS IN COMPLEX WITH CEFOTAXIME COMPND MOL_ID: 1; COMPND 2 MOLECULE: PENICILLIN-BINDING PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS EPIDERMIDIS (STRAIN ATCC 35984 / SOURCE 3 RP62A); SOURCE 4 ORGANISM_TAXID: 176279; SOURCE 5 GENE: PBP3, SERP1117; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS PENICILLIN-BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.SCHWINZER,H.BROGNARO,H.ROHDE,C.BETZEL REVDAT 1 13-DEC-23 8C5W 0 JRNL AUTH M.SCHWINZER,H.BROGNARO,H.ROHDE,C.BETZEL JRNL TITL STRUCTURE AND DYNAMICS OF THE PENICILLIN-BINDING PROTEIN 3 JRNL TITL 2 FROM STAPHYLOCOCCUS EPIDERMIDIS NATIVE AND IN COMPLEX WITH JRNL TITL 3 CEFOTAXIME AND VABORBACTAM JRNL REF INT J APPL BIOL PHARM 2023 JRNL DOI 10.26502/IJABPT.202127 REMARK 2 REMARK 2 RESOLUTION. 2.51 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 3 NUMBER OF REFLECTIONS : 64490 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.490 REMARK 3 FREE R VALUE TEST SET COUNT : 3542 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 46.7500 - 7.3200 1.00 2674 156 0.1802 0.1645 REMARK 3 2 7.3200 - 5.8100 1.00 2675 155 0.2273 0.2614 REMARK 3 3 5.8100 - 5.0800 1.00 2687 157 0.2128 0.2526 REMARK 3 4 5.0800 - 4.6100 1.00 2643 160 0.2026 0.2082 REMARK 3 5 4.6100 - 4.2800 1.00 2723 153 0.1991 0.2262 REMARK 3 6 4.2800 - 4.0300 1.00 2670 153 0.1974 0.2291 REMARK 3 7 4.0300 - 3.8300 1.00 2684 159 0.2086 0.2642 REMARK 3 8 3.8300 - 3.6600 1.00 2672 162 0.2092 0.2388 REMARK 3 9 3.6600 - 3.5200 1.00 2685 150 0.2245 0.2651 REMARK 3 10 3.5200 - 3.4000 1.00 2688 154 0.2386 0.3336 REMARK 3 11 3.4000 - 3.2900 1.00 2664 155 0.2943 0.3118 REMARK 3 12 3.2900 - 3.2000 1.00 2658 160 0.2949 0.2966 REMARK 3 13 3.2000 - 3.1200 1.00 2701 158 0.3153 0.3708 REMARK 3 14 3.1200 - 3.0400 1.00 2700 162 0.3407 0.3767 REMARK 3 15 3.0400 - 2.9700 1.00 2648 156 0.3760 0.4459 REMARK 3 16 2.9700 - 2.9100 1.00 2674 156 0.3871 0.4628 REMARK 3 17 2.9100 - 2.8500 1.00 2660 156 0.4106 0.4245 REMARK 3 18 2.8500 - 2.8000 1.00 2685 152 0.4260 0.4585 REMARK 3 19 2.8000 - 2.7500 0.99 2675 154 0.3795 0.3586 REMARK 3 20 2.7500 - 2.7000 0.97 2606 153 0.3835 0.3364 REMARK 3 21 2.7000 - 2.6600 0.87 2331 134 0.3767 0.4101 REMARK 3 22 2.6600 - 2.6100 0.69 1833 104 0.3743 0.3718 REMARK 3 23 2.6100 - 2.5800 0.65 1730 99 0.3933 0.3960 REMARK 3 24 2.5800 - 2.5400 0.42 1145 61 0.3950 0.4647 REMARK 3 25 2.5400 - 2.5100 0.16 437 23 0.4208 0.3880 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.510 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.085 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 90.32 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 100.2 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 : 0.018 5049 REMARK 3 ANGLE : 1.641 6809 REMARK 3 CHIRALITY : 0.071 751 REMARK 3 PLANARITY : 0.017 891 REMARK 3 DIHEDRAL : 9.876 691 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 8C5W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1292127863. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAY-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033210 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 70884 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 49.236 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.70 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 0.9900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.51 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE + CEFOTAXIME, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 154.43200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 41.53050 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 41.53050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 77.21600 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 41.53050 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 41.53050 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 231.64800 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 41.53050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.53050 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 77.21600 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 41.53050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.53050 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 231.64800 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 154.43200 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 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 GLY A 29 REMARK 465 SER A 30 REMARK 465 SER A 31 REMARK 465 HIS A 32 REMARK 465 HIS A 33 REMARK 465 HIS A 34 REMARK 465 HIS A 35 REMARK 465 HIS A 36 REMARK 465 HIS A 37 REMARK 465 SER A 38 REMARK 465 SER A 39 REMARK 465 GLY A 40 REMARK 465 GLU A 41 REMARK 465 ASN A 42 REMARK 465 LEU A 43 REMARK 465 TYR A 44 REMARK 465 PHE A 45 REMARK 465 GLN A 46 REMARK 465 ASP A 681 REMARK 465 ASN A 682 REMARK 465 LYS A 683 REMARK 465 LYS A 684 REMARK 465 ASP A 685 REMARK 465 ASP A 686 REMARK 465 SER A 687 REMARK 465 GLN A 688 REMARK 465 SER A 689 REMARK 465 ASN A 690 REMARK 465 ASN A 691 REMARK 465 GLU A 692 REMARK 465 GLU A 693 REMARK 465 LYS A 694 REMARK 465 GLU A 695 REMARK 465 ASP A 696 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER A 47 N CB OG REMARK 470 SER A 49 OG REMARK 470 HIS A 50 ND1 CD2 CE1 NE2 REMARK 470 TYR A 51 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 52 CG CD CE NZ REMARK 470 GLU A 208 CG CD OE1 OE2 REMARK 470 LYS A 254 CG CD CE NZ REMARK 470 ASN A 268 CG OD1 ND2 REMARK 470 LYS A 334 CG CD CE NZ REMARK 470 LYS A 600 CG CD CE NZ 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 H LYS A 52 O HOH A 801 1.09 REMARK 500 HH TYR A 403 OD2 ASP A 441 1.58 REMARK 500 O TYR A 209 HG SER A 213 1.58 REMARK 500 O ASN A 64 O HOH A 801 1.66 REMARK 500 OG SER A 607 OD1 ASN A 664 1.75 REMARK 500 OG SER A 392 O3 CEF A 701 1.87 REMARK 500 N LYS A 52 O HOH A 801 1.87 REMARK 500 O ILE A 381 OG1 THR A 385 2.18 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 GLU A 65 CD GLU A 65 OE1 -0.073 REMARK 500 GLU A 65 CD GLU A 65 OE2 -0.078 REMARK 500 VAL A 67 C PRO A 68 N 0.140 REMARK 500 GLU A 149 CD GLU A 149 OE1 0.067 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 GLU A 65 OE1 - CD - OE2 ANGL. DEV. = -12.4 DEGREES REMARK 500 ASP A 203 CB - CG - OD2 ANGL. DEV. = 8.7 DEGREES REMARK 500 LEU A 520 CB - CG - CD1 ANGL. DEV. = -11.3 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 SER A 49 62.80 176.07 REMARK 500 HIS A 50 108.73 -38.51 REMARK 500 LYS A 52 -72.17 -108.52 REMARK 500 ASN A 57 -129.33 -96.16 REMARK 500 SER A 88 123.72 -178.67 REMARK 500 ARG A 95 8.74 -66.94 REMARK 500 LYS A 96 36.34 -141.90 REMARK 500 THR A 97 98.75 -163.03 REMARK 500 SER A 98 -108.24 -109.57 REMARK 500 GLN A 99 -79.34 -28.31 REMARK 500 MET A 102 -79.36 -57.45 REMARK 500 THR A 110 22.32 -68.45 REMARK 500 GLU A 122 -47.26 -28.21 REMARK 500 LYS A 126 -72.82 -32.28 REMARK 500 SER A 135 -91.23 -47.87 REMARK 500 MET A 141 47.99 -100.97 REMARK 500 ASP A 150 -9.11 -57.68 REMARK 500 ARG A 163 28.81 -70.77 REMARK 500 LYS A 168 -109.38 -72.53 REMARK 500 LYS A 172 21.51 -66.65 REMARK 500 ALA A 190 -43.16 -142.71 REMARK 500 THR A 193 -138.89 90.07 REMARK 500 PRO A 196 78.74 -69.20 REMARK 500 ASN A 201 -65.64 -125.18 REMARK 500 SER A 217 -72.90 -45.83 REMARK 500 THR A 237 119.52 -38.86 REMARK 500 SER A 248 -40.11 55.41 REMARK 500 THR A 257 -177.30 -39.16 REMARK 500 GLU A 258 -75.86 58.37 REMARK 500 SER A 274 146.29 -174.10 REMARK 500 TYR A 275 -127.93 62.97 REMARK 500 LYS A 297 -134.88 52.94 REMARK 500 ARG A 300 135.74 -39.72 REMARK 500 SER A 303 158.04 170.80 REMARK 500 SER A 311 135.14 136.43 REMARK 500 MET A 347 136.29 -36.87 REMARK 500 ASP A 348 -4.55 -140.20 REMARK 500 ALA A 350 103.35 -168.06 REMARK 500 ASN A 359 11.13 -160.74 REMARK 500 ILE A 365 113.51 -161.07 REMARK 500 TYR A 379 54.45 -162.22 REMARK 500 SER A 392 8.38 -69.83 REMARK 500 LYS A 406 -3.11 73.19 REMARK 500 ASN A 432 65.34 -154.17 REMARK 500 ASN A 434 -32.32 -133.19 REMARK 500 ASP A 440 175.92 -59.22 REMARK 500 SER A 449 108.89 -58.04 REMARK 500 ALA A 461 35.14 -93.56 REMARK 500 PRO A 472 118.90 -39.04 REMARK 500 ASN A 501 36.09 73.18 REMARK 500 REMARK 500 THIS ENTRY HAS 61 RAMACHANDRAN OUTLIERS. 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 VAL A 632 ASN A 633 149.37 REMARK 500 PRO A 659 PRO A 660 121.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 93 0.18 SIDE CHAIN REMARK 500 ARG A 230 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 8C5W A 48 696 UNP Q5HNZ7 Q5HNZ7_STAEQ 48 696 SEQADV 8C5W GLY A 29 UNP Q5HNZ7 EXPRESSION TAG SEQADV 8C5W SER A 30 UNP Q5HNZ7 EXPRESSION TAG SEQADV 8C5W SER A 31 UNP Q5HNZ7 EXPRESSION TAG SEQADV 8C5W HIS A 32 UNP Q5HNZ7 EXPRESSION TAG SEQADV 8C5W HIS A 33 UNP Q5HNZ7 EXPRESSION TAG SEQADV 8C5W HIS A 34 UNP Q5HNZ7 EXPRESSION TAG SEQADV 8C5W HIS A 35 UNP Q5HNZ7 EXPRESSION TAG SEQADV 8C5W HIS A 36 UNP Q5HNZ7 EXPRESSION TAG SEQADV 8C5W HIS A 37 UNP Q5HNZ7 EXPRESSION TAG SEQADV 8C5W SER A 38 UNP Q5HNZ7 EXPRESSION TAG SEQADV 8C5W SER A 39 UNP Q5HNZ7 EXPRESSION TAG SEQADV 8C5W GLY A 40 UNP Q5HNZ7 EXPRESSION TAG SEQADV 8C5W GLU A 41 UNP Q5HNZ7 EXPRESSION TAG SEQADV 8C5W ASN A 42 UNP Q5HNZ7 EXPRESSION TAG SEQADV 8C5W LEU A 43 UNP Q5HNZ7 EXPRESSION TAG SEQADV 8C5W TYR A 44 UNP Q5HNZ7 EXPRESSION TAG SEQADV 8C5W PHE A 45 UNP Q5HNZ7 EXPRESSION TAG SEQADV 8C5W GLN A 46 UNP Q5HNZ7 EXPRESSION TAG SEQADV 8C5W SER A 47 UNP Q5HNZ7 EXPRESSION TAG SEQRES 1 A 668 GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY GLU SEQRES 2 A 668 ASN LEU TYR PHE GLN SER GLY SER HIS TYR LYS GLN LEU SEQRES 3 A 668 ILE LYS ASN ASP GLU ASN ILE THR VAL ASN GLU SER VAL SEQRES 4 A 668 PRO ARG GLY ARG ILE LEU ASP ARG ASN GLY LYS VAL LEU SEQRES 5 A 668 VAL ASP ASN ALA SER LYS MET SER ILE THR TYR THR ARG SEQRES 6 A 668 ASN ARG LYS THR SER GLN LYS GLU MET LEU ASN THR ALA SEQRES 7 A 668 LYS LYS LEU THR ASP LEU ILE LYS MET ASP THR ASP LYS SEQRES 8 A 668 ILE THR GLU ARG ASP LYS LYS ASP PHE TRP ILE GLN MET SEQRES 9 A 668 TYR PRO SER SER ALA LYS LYS LEU MET ARG LYS GLU GLN SEQRES 10 A 668 LEU MET LEU GLU ASP GLY SER ILE SER GLN ASP GLN PHE SEQRES 11 A 668 ASP THR GLN LEU ARG ASP LYS ILE GLY LYS LYS GLN LEU SEQRES 12 A 668 LYS GLN LEU THR LYS LYS ASP LEU GLN VAL LEU ALA ILE SEQRES 13 A 668 TYR ARG GLU MET ASN ALA GLY SER THR LEU ASP PRO GLN SEQRES 14 A 668 THR ILE LYS ASN GLU ASP VAL SER GLU LYS GLU TYR ALA SEQRES 15 A 668 ALA VAL SER GLN GLN LEU SER LYS LEU PRO GLY VAL ASN SEQRES 16 A 668 THR THR MET ASP TRP ASP ARG LYS TYR PRO TYR GLY ASP SEQRES 17 A 668 THR LEU ARG GLY ILE PHE GLY ASP VAL SER THR SER THR SEQRES 18 A 668 GLU GLY ILE PRO LYS GLU LEU THR GLU GLN TYR LEU SER SEQRES 19 A 668 LYS GLY TYR SER ARG ASN ASP ARG VAL GLY LYS SER TYR SEQRES 20 A 668 LEU GLU TYR GLN TYR GLU ASP VAL LEU LYS GLY THR LYS SEQRES 21 A 668 LYS GLN MET LYS TYR THR THR ASP LYS SER GLY ARG VAL SEQRES 22 A 668 ILE SER SER GLU VAL LEU ASN PRO GLY SER ARG GLY HIS SEQRES 23 A 668 ASP LEU GLN LEU THR ILE ASP ILE ASP LEU GLN LYS LYS SEQRES 24 A 668 VAL GLU SER LEU LEU GLU LYS GLN ILE SER LYS LEU ARG SEQRES 25 A 668 SER GLN GLY ALA LYS ASP MET ASP ASN ALA LEU MET VAL SEQRES 26 A 668 VAL GLN ASN PRO LYS ASN GLY ASP ILE LEU ALA ILE ALA SEQRES 27 A 668 GLY LYS GLN ILE ASP LYS GLN GLY LYS LEU LYS ASP TYR SEQRES 28 A 668 ASP ILE GLY ASN PHE THR ALA GLN TYR THR VAL GLY SER SEQRES 29 A 668 SER VAL LYS GLY GLY THR LEU LEU ALA GLY TYR GLN ASN SEQRES 30 A 668 LYS ALA ILE ASN VAL GLY GLU THR MET VAL ASP GLU PRO SEQRES 31 A 668 LEU LYS PHE GLN GLY GLY LEU THR LYS ARG SER TYR PHE SEQRES 32 A 668 ASN LYS ASN GLY HIS VAL SER ILE ASP ASP LYS GLN ALA SEQRES 33 A 668 LEU MET HIS SER SER ASN VAL TYR MET PHE LYS THR ALA SEQRES 34 A 668 LEU LYS LEU ALA GLY ASP PRO TYR THR SER GLY MET SER SEQRES 35 A 668 LEU PRO ASN ASN ILE ALA ASP ALA GLY ARG LYS LEU ARG SEQRES 36 A 668 LYS GLY LEU ASN GLN VAL GLY LEU GLY LEU LYS THR GLY SEQRES 37 A 668 ILE ASP LEU PRO ASN GLU THR PRO GLY GLN ILE GLU PRO SEQRES 38 A 668 LEU THR ASN ASN PRO GLY ASN TYR LEU ASP LEU ALA ILE SEQRES 39 A 668 GLY GLN TYR ASP THR TYR THR PRO LEU GLN LEU SER GLN SEQRES 40 A 668 TYR VAL SER THR ILE ALA ASN ASP GLY TYR ARG ILE GLN SEQRES 41 A 668 PRO HIS ILE GLY LEU SER ILE TYR GLU SER THR ASN LYS SEQRES 42 A 668 ASP GLU THR GLY PRO LEU LYS ARG LYS ILE LYS GLY ASN SEQRES 43 A 668 VAL LEU ASN LYS VAL ASN ASN SER ASN ASP GLU ILE LYS SEQRES 44 A 668 GLU VAL GLN GLU GLY PHE LYS MET ALA PHE ASN GLU LYS SEQRES 45 A 668 GLN GLY THR GLY TYR ALA SER PHE ARG ASN THR VAL VAL SEQRES 46 A 668 PRO SER ALA GLY LYS THR GLY THR ALA GLU VAL PHE GLN SEQRES 47 A 668 ASP GLY GLU PRO ARG VAL ASN SER THR TYR ILE GLY TYR SEQRES 48 A 668 ALA PRO VAL ASP ASP PRO LYS LEU SER PHE SER ILE VAL SEQRES 49 A 668 TYR THR ASN GLN PRO VAL PRO PRO PRO TRP LEU ASN GLY SEQRES 50 A 668 GLY ASP LEU GLY ARG ASP VAL ILE ASN TYR TYR PHE LYS SEQRES 51 A 668 ASP LYS ASP ASN LYS LYS ASP ASP SER GLN SER ASN ASN SEQRES 52 A 668 GLU GLU LYS GLU ASP HET CEF A 701 26 HETNAM CEF CEFOTAXIME, C3' CLEAVED, OPEN, BOUND FORM FORMUL 2 CEF C14 H15 N5 O5 S2 FORMUL 3 HOH *5(H2 O) HELIX 1 AA1 SER A 98 THR A 110 1 13 HELIX 2 AA2 THR A 121 TYR A 133 1 13 HELIX 3 AA3 TYR A 133 LYS A 139 1 7 HELIX 4 AA4 MET A 141 GLY A 151 1 11 HELIX 5 AA5 SER A 154 ARG A 163 1 10 HELIX 6 AA6 LYS A 168 LYS A 172 5 5 HELIX 7 AA7 THR A 175 MET A 188 1 14 HELIX 8 AA8 SER A 205 GLN A 214 1 10 HELIX 9 AA9 LEU A 238 GLY A 243 1 6 HELIX 10 AB1 SER A 274 TYR A 280 1 7 HELIX 11 AB2 TYR A 280 LYS A 285 1 6 HELIX 12 AB3 ASP A 321 SER A 341 1 21 HELIX 13 AB4 ILE A 381 ALA A 386 1 6 HELIX 14 AB5 GLY A 391 SER A 393 5 3 HELIX 15 AB6 VAL A 394 ASN A 405 1 12 HELIX 16 AB7 GLN A 422 GLY A 424 5 3 HELIX 17 AB8 SER A 429 LYS A 433 5 5 HELIX 18 AB9 ASP A 440 SER A 448 1 9 HELIX 19 AC1 SER A 449 ALA A 461 1 13 HELIX 20 AC2 ILE A 475 VAL A 489 1 15 HELIX 21 AC3 ASN A 513 ALA A 521 1 9 HELIX 22 AC4 THR A 529 ASN A 542 1 14 HELIX 23 AC5 SER A 582 GLU A 599 1 18 HELIX 24 AC6 GLY A 604 ARG A 609 1 6 HELIX 25 AC7 GLY A 666 PHE A 677 1 12 SHEET 1 AA1 2 GLN A 53 LYS A 56 0 SHEET 2 AA1 2 ILE A 61 ASN A 64 -1 O THR A 62 N ILE A 55 SHEET 1 AA2 3 THR A 198 LYS A 200 0 SHEET 2 AA2 3 VAL A 79 TYR A 91 -1 N ILE A 89 O ILE A 199 SHEET 3 AA2 3 VAL A 222 LYS A 231 -1 O ASP A 229 N ALA A 84 SHEET 1 AA3 6 THR A 198 LYS A 200 0 SHEET 2 AA3 6 VAL A 79 TYR A 91 -1 N ILE A 89 O ILE A 199 SHEET 3 AA3 6 ILE A 72 LEU A 73 -1 N ILE A 72 O LEU A 80 SHEET 4 AA3 6 ASP A 315 LEU A 318 1 O LEU A 318 N LEU A 73 SHEET 5 AA3 6 GLY A 552 TYR A 556 -1 O SER A 554 N GLN A 317 SHEET 6 AA3 6 LEU A 567 LYS A 570 -1 O ARG A 569 N ILE A 555 SHEET 1 AA4 2 GLN A 290 LYS A 292 0 SHEET 2 AA4 2 GLU A 305 ASN A 308 -1 O ASN A 308 N GLN A 290 SHEET 1 AA5 6 LYS A 377 ASP A 378 0 SHEET 2 AA5 6 ILE A 362 GLN A 369 -1 N GLN A 369 O LYS A 377 SHEET 3 AA5 6 ASN A 349 GLN A 355 -1 N MET A 352 O ALA A 366 SHEET 4 AA5 6 LEU A 647 PRO A 657 -1 O SER A 648 N GLN A 355 SHEET 5 AA5 6 GLU A 629 ALA A 640 -1 N GLY A 638 O PHE A 649 SHEET 6 AA5 6 ALA A 616 GLY A 620 -1 N GLY A 620 O THR A 635 SHEET 1 AA6 6 LYS A 377 ASP A 378 0 SHEET 2 AA6 6 ILE A 362 GLN A 369 -1 N GLN A 369 O LYS A 377 SHEET 3 AA6 6 ASN A 349 GLN A 355 -1 N MET A 352 O ALA A 366 SHEET 4 AA6 6 LEU A 647 PRO A 657 -1 O SER A 648 N GLN A 355 SHEET 5 AA6 6 GLU A 629 ALA A 640 -1 N GLY A 638 O PHE A 649 SHEET 6 AA6 6 GLU A 623 GLN A 626 -1 N VAL A 624 O ARG A 631 SHEET 1 AA7 2 MET A 414 ASP A 416 0 SHEET 2 AA7 2 VAL A 437 ILE A 439 -1 O VAL A 437 N ASP A 416 SHEET 1 AA8 2 LEU A 419 LYS A 420 0 SHEET 2 AA8 2 THR A 426 LYS A 427 -1 O LYS A 427 N LEU A 419 SHEET 1 AA9 2 TYR A 545 ILE A 547 0 SHEET 2 AA9 2 VAL A 575 LYS A 578 -1 O LEU A 576 N ARG A 546 LINK OG SER A 392 C8 CEF A 701 1555 1555 1.37 CISPEP 1 ALA A 640 PRO A 641 0 -0.85 CRYST1 83.061 83.061 308.864 90.00 90.00 90.00 P 41 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 0.012039 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012039 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003238 0.00000