HEADER PENICILLIN-BINDING PROTEIN 17-DEC-12 3ZGA TITLE CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 4 FROM LISTERIA TITLE 2 MONOCYTOGENES IN THE CARBENICILLIN BOUND FORM CAVEAT 3ZGA CB9 A 801 IS PLANAR AT ATOM CB COMPND MOL_ID: 1; COMPND 2 MOLECULE: PENICILLIN-BINDING PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 73-119; COMPND 5 SYNONYM: LMO2229 PROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: PROTEOLYSIS FROM 120-177; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: PENICILLIN-BINDING PROTEIN 4; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: RESIDUES 178-714; COMPND 12 SYNONYM: LMO2229 PROTEIN; COMPND 13 ENGINEERED: YES; COMPND 14 OTHER_DETAILS: CARBENICILLIN BOUND TO SER394, PROTEOLYSIS FROM 120- COMPND 15 177 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LISTERIA MONOCYTOGENES; SOURCE 3 ORGANISM_TAXID: 1639; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VARIANT: RIL; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPROEXHTA; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: LISTERIA MONOCYTOGENES; SOURCE 12 ORGANISM_TAXID: 1639; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 15 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 16 EXPRESSION_SYSTEM_VARIANT: RIL; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PPROEXHTA KEYWDS PENICILLIN-BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.H.JEONG,Y.G.KIM REVDAT 3 20-DEC-23 3ZGA 1 REMARK LINK REVDAT 2 31-JUL-13 3ZGA 1 JRNL REVDAT 1 29-MAY-13 3ZGA 0 JRNL AUTH J.JEONG,Y.KIM,C.ROJVIRIYA,S.HA,B.S.KANG,Y.KIM JRNL TITL CRYSTAL STRUCTURES OF BIFUNCTIONAL PENICILLIN-BINDING JRNL TITL 2 PROTEIN 4 FROM LISTERIA MONOCYTOGENES. JRNL REF ANTIMICROB.AGENTS CHEMOTHER. V. 57 3507 2013 JRNL REFN ISSN 0066-4804 JRNL PMID 23669378 JRNL DOI 10.1128/AAC.00144-13 REMARK 2 REMARK 2 RESOLUTION. 2.01 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) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.73 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.500 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 39477 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 26.7283 - 4.8234 1.00 2938 157 0.1610 0.1739 REMARK 3 2 4.8234 - 3.8321 1.00 2821 150 0.1377 0.1811 REMARK 3 3 3.8321 - 3.3487 1.00 2777 148 0.1706 0.2280 REMARK 3 4 3.3487 - 3.0430 1.00 2745 147 0.1952 0.2313 REMARK 3 5 3.0430 - 2.8252 0.99 2744 146 0.2006 0.2599 REMARK 3 6 2.8252 - 2.6588 0.99 2717 145 0.1935 0.2624 REMARK 3 7 2.6588 - 2.5257 0.99 2732 146 0.1975 0.2639 REMARK 3 8 2.5257 - 2.4158 0.99 2699 145 0.2058 0.2484 REMARK 3 9 2.4158 - 2.3229 0.99 2700 144 0.2116 0.2469 REMARK 3 10 2.3229 - 2.2428 0.99 2674 142 0.2221 0.2260 REMARK 3 11 2.2428 - 2.1727 0.98 2667 143 0.2247 0.2718 REMARK 3 12 2.1727 - 2.1106 0.95 2576 137 0.2512 0.2883 REMARK 3 13 2.1106 - 2.0551 0.89 2417 129 0.2706 0.2953 REMARK 3 14 2.0551 - 2.0049 0.84 2270 121 0.2842 0.3319 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.330 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.31 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.50 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 : 0.008 3904 REMARK 3 ANGLE : 1.107 5294 REMARK 3 CHIRALITY : 0.071 588 REMARK 3 PLANARITY : 0.005 687 REMARK 3 DIHEDRAL : 17.144 1447 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 11.3640 -22.0677 -11.0694 REMARK 3 T TENSOR REMARK 3 T11: 0.1940 T22: 0.3119 REMARK 3 T33: 0.2140 T12: 0.0004 REMARK 3 T13: -0.0493 T23: -0.0257 REMARK 3 L TENSOR REMARK 3 L11: 1.1010 L22: 1.4672 REMARK 3 L33: 1.8659 L12: 0.4090 REMARK 3 L13: -0.2838 L23: -1.0092 REMARK 3 S TENSOR REMARK 3 S11: 0.0303 S12: -0.0271 S13: 0.1697 REMARK 3 S21: -0.0194 S22: -0.0056 S23: 0.1006 REMARK 3 S31: -0.1339 S32: -0.0085 S33: -0.0295 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 3ZGA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-DEC-12. REMARK 100 THE DEPOSITION ID IS D_1290055149. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAR-10 REMARK 200 TEMPERATURE (KELVIN) : 295 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39480 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 24.900 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.9000 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) : 2.08 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.30000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.100 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: PDB ENTRY 3ZG7 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 24.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% POLYETHYLENE GLYCOL 3350, 0.1M REMARK 280 AMMONIUM TARTRATE (PH 7.0) REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 42.40650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 63.88850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 42.40650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 63.88850 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.8 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 73 REMARK 465 LEU A 74 REMARK 465 GLU A 75 REMARK 465 SER A 76 REMARK 465 ARG A 118 REMARK 465 LYS A 119 REMARK 465 ARG B 178 REMARK 465 GLU B 179 REMARK 465 ILE B 180 REMARK 465 GLU B 181 REMARK 465 LYS B 182 REMARK 465 THR B 183 REMARK 465 LYS B 642 REMARK 465 SER B 643 REMARK 465 ALA B 644 REMARK 465 ASP B 645 REMARK 465 PHE B 646 REMARK 465 SER B 647 REMARK 465 THR B 648 REMARK 465 LYS B 649 REMARK 465 SER B 650 REMARK 465 ALA B 651 REMARK 465 ALA B 652 REMARK 465 GLN B 653 REMARK 465 GLU B 654 REMARK 465 THR B 655 REMARK 465 ALA B 656 REMARK 465 ALA B 657 REMARK 465 LYS B 658 REMARK 465 LYS B 659 REMARK 465 GLU B 660 REMARK 465 GLU B 661 REMARK 465 GLU B 662 REMARK 465 GLU B 663 REMARK 465 LYS B 664 REMARK 465 GLU B 665 REMARK 465 LYS B 666 REMARK 465 ASN B 667 REMARK 465 SER B 668 REMARK 465 GLY B 669 REMARK 465 SER B 670 REMARK 465 ASP B 671 REMARK 465 PHE B 672 REMARK 465 TRP B 673 REMARK 465 SER B 674 REMARK 465 GLY B 675 REMARK 465 VAL B 676 REMARK 465 LYS B 677 REMARK 465 GLU B 678 REMARK 465 LYS B 679 REMARK 465 ALA B 680 REMARK 465 ASP B 681 REMARK 465 GLU B 682 REMARK 465 ALA B 683 REMARK 465 GLY B 684 REMARK 465 GLU B 685 REMARK 465 THR B 686 REMARK 465 ILE B 687 REMARK 465 LYS B 688 REMARK 465 LYS B 689 REMARK 465 GLY B 690 REMARK 465 ALA B 691 REMARK 465 ASP B 692 REMARK 465 LYS B 693 REMARK 465 VAL B 694 REMARK 465 LYS B 695 REMARK 465 GLU B 696 REMARK 465 PHE B 697 REMARK 465 GLY B 698 REMARK 465 GLY B 699 REMARK 465 LYS B 700 REMARK 465 VAL B 701 REMARK 465 SER B 702 REMARK 465 ASP B 703 REMARK 465 GLY B 704 REMARK 465 ILE B 705 REMARK 465 GLY B 706 REMARK 465 ASN B 707 REMARK 465 LEU B 708 REMARK 465 ILE B 709 REMARK 465 ASP B 710 REMARK 465 SER B 711 REMARK 465 ILE B 712 REMARK 465 GLY B 713 REMARK 465 ASN B 714 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 OG SER A 105 OD1 ASN A 107 2.06 REMARK 500 OG SER B 394 O CB9 B 801 2.11 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 95 -0.38 63.04 REMARK 500 GLU A 116 -130.12 52.75 REMARK 500 ALA B 235 86.08 -156.79 REMARK 500 VAL B 401 -67.26 -122.26 REMARK 500 LYS B 424 129.63 -34.74 REMARK 500 PRO B 582 47.42 -79.23 REMARK 500 ASP B 585 -1.02 66.27 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 B 1642 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1643 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1644 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: Binding site for Ligand CB9 B 801 bound to SER B REMARK 800 394 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZG7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 4 FROM LISTERIA REMARK 900 MONOCYTOGENES IN THE APO FORM REMARK 900 RELATED ID: 3ZG8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PENICILLIN BINDING PROTEIN 4 FROM LISTERIA REMARK 900 MONOCYTOGENES IN THE AMPICILLIN BOUND FORM REMARK 900 RELATED ID: 3ZG9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 4 FROM LISTERIA REMARK 900 MONOCYTOGENES IN THE CEFUROXIME BOUND FORM DBREF 3ZGA A 73 119 UNP Q8Y547 Q8Y547_LISMO 73 119 DBREF 3ZGA B 178 714 UNP Q8Y547 Q8Y547_LISMO 178 714 SEQRES 1 A 47 GLY LEU GLU SER ALA THR ILE ILE TYR ASP LYS ASP GLY SEQRES 2 A 47 ASP LYS ALA GLY GLU LEU SER SER THR ASP ALA THR PHE SEQRES 3 A 47 VAL SER ILE ASP LYS ILE SER LYS ASN LEU GLN ASN ALA SEQRES 4 A 47 VAL VAL SER ILE GLU ASP ARG LYS SEQRES 1 B 537 ARG GLU ILE GLU LYS THR TYR SER LYS ASP GLU ILE MET SEQRES 2 B 537 GLU MET TYR LEU ASN ARG SER TYR PHE GLY ASN GLY GLU SEQRES 3 B 537 TRP GLY VAL GLU ASN ALA SER LEU LYS TYR PHE GLY LYS SEQRES 4 B 537 SER ALA ALA ASP LEU ASN ILE PRO GLU ALA ALA THR ILE SEQRES 5 B 537 ALA GLY LEU LEU GLN ALA PRO SER ALA TYR ASP PRO TYR SEQRES 6 B 537 GLN HIS ILE ASP LYS ALA THR ASN ARG ARG ASN MET VAL SEQRES 7 B 537 LEU ASN ALA MET VAL GLU THR GLY THR ILE SER LYS ALA SEQRES 8 B 537 GLU GLY ASP LYS TYR LYS ALA THR LYS ILE VAL LEU ASN SEQRES 9 B 537 ASP GLN SER LYS ASP PRO LEU ALA ASN LYS TYR PRO TRP SEQRES 10 B 537 TYR VAL ASP ALA VAL ILE ASN GLU ALA VAL ASN GLU ALA SEQRES 11 B 537 ASP ILE THR GLN ASP GLU ILE MET GLN LYS GLY TYR LYS SEQRES 12 B 537 ILE TYR THR GLU LEU ASP GLN ASN TYR GLN THR SER LEU SEQRES 13 B 537 GLU ASN VAL TYR ASN ASN ASP GLY LEU PHE PRO SER ASN SEQRES 14 B 537 ALA ASN ASP GLY THR LEU VAL GLN SER GLY ALA VAL LEU SEQRES 15 B 537 MET ASP PRO ALA THR GLY GLY ILE ARG ALA LEU VAL GLY SEQRES 16 B 537 GLY ARG GLY GLU HIS VAL PHE ARG GLY PHE ASN ARG ALA SEQRES 17 B 537 THR GLN MET LYS ALA GLN PRO GLY SER THR MET LYS PRO SEQRES 18 B 537 LEU ALA VAL TYR THR PRO ALA LEU GLN SER GLY TYR ASP SEQRES 19 B 537 VAL ASP SER MET LEU LYS ASP GLU LYS ILE THR TYR LYS SEQRES 20 B 537 GLY ASN TYR THR PRO THR ASN VAL GLY GLY VAL TYR SER SEQRES 21 B 537 GLY GLU VAL PRO MET TYR LYS ALA VAL ALA ASN SER ILE SEQRES 22 B 537 ASN ALA PRO ALA VAL TRP LEU LEU ASP GLN ILE GLY ILE SEQRES 23 B 537 ASP LYS GLY VAL LYS SER VAL GLU LYS PHE GLY ILE THR SEQRES 24 B 537 VAL PRO GLU LYS ASP ARG THR LEU GLY LEU ALA LEU GLY SEQRES 25 B 537 GLY MET SER LYS GLY ALA SER PRO VAL GLU MET ALA THR SEQRES 26 B 537 ALA TYR ALA THR PHE ALA ASN ASN GLY ALA LYS PRO GLU SEQRES 27 B 537 SER HIS ILE ILE THR LYS ILE VAL ASP PRO SER GLY ASN SEQRES 28 B 537 THR VAL TYR GLU ASN VAL PRO LYS THR LYS GLN ILE ILE SEQRES 29 B 537 SER GLU THR VAL SER ASN GLU MET THR SER MET LEU LEU SEQRES 30 B 537 ASP VAL ILE ASN THR GLY THR GLY GLN SER ALA ALA VAL SEQRES 31 B 537 SER GLY HIS GLU MET ALA GLY LYS THR GLY SER THR GLN SEQRES 32 B 537 VAL PRO PHE ASP ASP THR SER GLY THR LYS ASP GLN TRP SEQRES 33 B 537 PHE VAL GLY TYR THR PRO ASN LEU VAL GLY ALA VAL TRP SEQRES 34 B 537 MET GLY TYR ASP LYS THR ASP LYS GLU HIS TYR LEU THR SEQRES 35 B 537 THR THR SER SER ALA GLY VAL SER SER LEU ALA HIS TYR SEQRES 36 B 537 VAL MET ASN SER GLY LEU GLN TYR GLN LYS SER ALA ASP SEQRES 37 B 537 PHE SER THR LYS SER ALA ALA GLN GLU THR ALA ALA LYS SEQRES 38 B 537 LYS GLU GLU GLU GLU LYS GLU LYS ASN SER GLY SER ASP SEQRES 39 B 537 PHE TRP SER GLY VAL LYS GLU LYS ALA ASP GLU ALA GLY SEQRES 40 B 537 GLU THR ILE LYS LYS GLY ALA ASP LYS VAL LYS GLU PHE SEQRES 41 B 537 GLY GLY LYS VAL SER ASP GLY ILE GLY ASN LEU ILE ASP SEQRES 42 B 537 SER ILE GLY ASN HET CB9 B 801 26 HET GOL B1642 6 HET GOL B1643 6 HET GOL B1644 6 HETNAM CB9 (2R,4S)-2-[(1R)-1-{[(2S)-2-CARBOXY-2- HETNAM 2 CB9 PHENYLACETYL]AMINO}-2-OXOETHYL]-5,5-DIMETHYL-1,3- HETNAM 3 CB9 THIAZOLIDINE-4-CARBOXYLIC ACID HETNAM GOL GLYCEROL HETSYN CB9 BOUND FORM OF CARBENICILLIN HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 CB9 C17 H20 N2 O6 S FORMUL 4 GOL 3(C3 H8 O3) FORMUL 7 HOH *114(H2 O) HELIX 1 1 SER A 100 ILE A 104 5 5 HELIX 2 2 SER A 105 SER A 114 1 10 HELIX 3 3 SER B 185 SER B 197 1 13 HELIX 4 4 TRP B 204 GLY B 215 1 12 HELIX 5 5 ASN B 222 LEU B 233 1 12 HELIX 6 6 HIS B 244 GLU B 261 1 18 HELIX 7 7 SER B 266 THR B 276 1 11 HELIX 8 8 TYR B 292 ALA B 307 1 16 HELIX 9 9 THR B 310 LYS B 317 1 8 HELIX 10 10 ASP B 326 ASN B 338 1 13 HELIX 11 11 ASN B 339 PHE B 343 5 5 HELIX 12 12 PRO B 392 THR B 395 5 4 HELIX 13 13 MET B 396 VAL B 401 1 6 HELIX 14 14 VAL B 401 GLN B 407 1 7 HELIX 15 15 MET B 442 ASN B 448 1 7 HELIX 16 16 ILE B 450 GLY B 462 1 13 HELIX 17 17 GLY B 462 PHE B 473 1 12 HELIX 18 18 PRO B 478 ARG B 482 5 5 HELIX 19 19 THR B 483 GLY B 489 5 7 HELIX 20 20 SER B 496 ASN B 509 1 14 HELIX 21 21 SER B 542 THR B 559 1 18 HELIX 22 22 GLY B 562 ALA B 566 5 5 HELIX 23 23 SER B 623 GLN B 639 1 17 SHEET 1 AA 5 LYS A 87 LEU A 91 0 SHEET 2 AA 5 THR A 78 TYR A 81 -1 O THR A 78 N LEU A 91 SHEET 3 AA 5 LYS B 320 THR B 323 1 O ILE B 321 N TYR A 81 SHEET 4 AA 5 ILE B 519 VAL B 523 -1 N THR B 520 O TYR B 322 SHEET 5 AA 5 THR B 529 GLU B 532 -1 N VAL B 530 O ILE B 522 SHEET 1 BA 5 GLY B 366 VAL B 371 0 SHEET 2 BA 5 GLN B 354 ASP B 361 -1 O ALA B 357 N VAL B 371 SHEET 3 BA 5 LEU B 601 GLY B 608 -1 O VAL B 602 N MET B 360 SHEET 4 BA 5 THR B 589 THR B 598 -1 O GLN B 592 N MET B 607 SHEET 5 BA 5 ALA B 573 GLN B 580 -1 O ALA B 573 N TYR B 597 SHEET 1 BB 2 MET B 415 ASP B 418 0 SHEET 2 BB 2 GLY B 438 PRO B 441 -1 O GLY B 438 N ASP B 418 SHEET 1 BC 2 ALA B 512 PRO B 514 0 SHEET 2 BC 2 THR B 537 GLN B 539 -1 O LYS B 538 N LYS B 513 LINK OG SER B 394 C CB9 B 801 1555 1555 1.41 SITE 1 AC1 4 ALA B 347 ASN B 348 GLU B 615 TYR B 617 SITE 1 AC2 5 LYS B 389 ALA B 390 GLN B 391 ASP B 591 SITE 2 AC2 5 HOH B2104 SITE 1 AC3 3 PRO B 429 THR B 430 CB9 B 801 SITE 1 AC4 11 SER B 394 VAL B 432 SER B 449 ASN B 451 SITE 2 AC4 11 THR B 576 GLY B 577 SER B 578 THR B 579 SITE 3 AC4 11 GLN B 580 SER B 623 GOL B1644 CRYST1 84.813 127.777 54.661 90.00 90.00 90.00 P 21 21 2 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 0.011791 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007826 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018295 0.00000