HEADER HYDROLASE 14-DEC-10 2Y2B TITLE CRYSTAL STRUCTURE OF AMPD IN COMPLEX WITH REACTION PRODUCTS CAVEAT 2Y2B AH0 A 1000 HAS WRONG CHIRALITY AT ATOM CA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 1,6-ANHYDRO-N-ACETYLMURAMYL-L-ALANINE AMIDASE AMPD; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: AMPD, N-ACETYLMURAMOYL-L-ALANINE AMIDASE; COMPND 5 EC: 3.5.1.28; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CITROBACTER FREUNDII; SOURCE 3 ORGANISM_TAXID: 546; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE, PEPTIDOGLYCAN AMIDASE, AMIDASE_2 FAMILY, ACTIVATION KEYWDS 2 MECHANISM EXPDTA X-RAY DIFFRACTION AUTHOR C.CARRASCO-LOPEZ,A.ROJAS-ALTUVE,W.ZHANG,D.HESEK,M.LEE,S.BARBE, AUTHOR 2 I.ANDRE,N.SILVA-MARTIN,M.MARTINEZ-RIPOLL,S.MOBASHERY,J.A.HERMOSO REVDAT 4 31-JAN-24 2Y2B 1 REMARK REVDAT 3 02-NOV-22 2Y2B 1 LINK REVDAT 2 14-SEP-11 2Y2B 1 JRNL REVDAT 1 20-JUL-11 2Y2B 0 JRNL AUTH C.CARRASCO-LOPEZ,A.ROJAS-ALTUVE,W.ZHANG,D.HESEK,M.LEE, JRNL AUTH 2 S.BARBE,I.ANDRE,P.FERRER,N.SILVA-MARTIN,G.R.CASTRO, JRNL AUTH 3 M.MARTINEZ-RIPOLL,S.MOBASHERY,J.A.HERMOSO JRNL TITL CRYSTAL STRUCTURES OF BACTERIAL PEPTIDOGLYCAN AMIDASE AMPD JRNL TITL 2 AND AN UNPRECEDENTED ACTIVATION MECHANISM. JRNL REF J.BIOL.CHEM. V. 286 31714 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21775432 JRNL DOI 10.1074/JBC.M111.264366 REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.020 REMARK 3 COMPLETENESS FOR RANGE (%) : 77.0 REMARK 3 NUMBER OF REFLECTIONS : 31507 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.200 REMARK 3 FREE R VALUE TEST SET COUNT : 2845 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 58.7290 - 3.6634 1.00 4892 349 0.1720 0.2080 REMARK 3 2 3.6634 - 2.9078 1.00 4903 358 0.1691 0.2226 REMARK 3 3 2.9078 - 2.5402 1.00 4875 361 0.1686 0.2127 REMARK 3 4 2.5402 - 2.3079 1.00 4848 375 0.1577 0.2189 REMARK 3 5 2.3079 - 2.1425 0.98 4698 406 0.1589 0.2299 REMARK 3 6 2.1425 - 2.0162 0.89 4320 361 0.1610 0.2290 REMARK 3 7 2.0162 - 1.9152 0.74 3619 275 0.1737 0.2323 REMARK 3 8 1.9152 - 1.8318 0.51 2456 205 0.1826 0.2590 REMARK 3 9 1.8318 - 1.7613 0.29 1414 104 0.1932 0.2580 REMARK 3 10 1.7613 - 1.7005 0.11 530 51 0.2387 0.3418 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 : 0.39 REMARK 3 B_SOL : 40.81 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.48740 REMARK 3 B22 (A**2) : 1.48740 REMARK 3 B33 (A**2) : -2.97470 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 : 0.014 4451 REMARK 3 ANGLE : 1.121 6096 REMARK 3 CHIRALITY : 0.073 645 REMARK 3 PLANARITY : 0.013 807 REMARK 3 DIHEDRAL : 17.240 1627 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: LIGANDS WERE FOUND IN MOLECULE A REMARK 4 REMARK 4 2Y2B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-DEC-10. REMARK 100 THE DEPOSITION ID IS D_1290046732. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97627 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 : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31507 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.18000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2Y28 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS PH 6.0, 0.1M LI2SO4, 28% PEG REMARK 280 3350 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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 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 61.89067 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 30.94533 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 PRO A 180 REMARK 465 SER A 181 REMARK 465 SER A 182 REMARK 465 HIS A 183 REMARK 465 LYS A 184 REMARK 465 GLU A 185 REMARK 465 MET A 186 REMARK 465 THR A 187 REMARK 465 SER B 182 REMARK 465 HIS B 183 REMARK 465 LYS B 184 REMARK 465 GLU B 185 REMARK 465 MET B 186 REMARK 465 THR B 187 REMARK 465 SER C 182 REMARK 465 HIS C 183 REMARK 465 LYS C 184 REMARK 465 GLU C 185 REMARK 465 MET C 186 REMARK 465 THR C 187 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 ASP A 164 CB - CG - OD1 ANGL. DEV. = 6.0 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 TRP A 95 73.89 -110.40 REMARK 500 GLU A 160 15.57 59.57 REMARK 500 TRP B 95 76.86 -108.63 REMARK 500 THR B 179 72.87 43.17 REMARK 500 ASP C 25 51.23 21.01 REMARK 500 TRP C 95 76.89 -106.59 REMARK 500 ARG C 161 -42.36 -130.29 REMARK 500 THR C 179 96.34 32.42 REMARK 500 PRO C 180 8.12 -64.69 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 B 487 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH C 462 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH C 463 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH C 464 DISTANCE = 8.00 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 ZN A 203 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 34 ND1 REMARK 620 2 HIS A 154 ND1 94.2 REMARK 620 3 ASP A 164 OD1 146.9 86.3 REMARK 620 4 ASP A 164 OD2 102.0 130.1 55.5 REMARK 620 5 AH0 A 201 O 99.8 157.8 91.2 63.5 REMARK 620 6 AH0 A 201 OXT 115.0 106.5 96.4 108.4 51.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 34 ND1 REMARK 620 2 HIS B 154 ND1 90.8 REMARK 620 3 ASP B 164 OD2 101.7 133.8 REMARK 620 4 ASP B 164 OD1 145.2 89.5 55.8 REMARK 620 5 HOH B 450 O 114.3 101.2 113.0 99.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 34 ND1 REMARK 620 2 HIS C 154 ND1 93.7 REMARK 620 3 ASP C 164 OD1 144.2 88.5 REMARK 620 4 ASP C 164 OD2 98.3 133.7 57.1 REMARK 620 5 HOH C 430 O 110.6 102.6 103.8 114.2 REMARK 620 N 1 2 3 4 REMARK 630 REMARK 630 MOLECULE TYPE: NULL REMARK 630 MOLECULE NAME: L-ALA-GAMMA-D-GLU-MESO-DIAMINOPIMELIC ACID REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 MHI A 202 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: ALA DGL API REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AH0 A 1000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MHI A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1180 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1180 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 1180 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1J3G RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF CITROBACTER FREUNDII AMPD REMARK 900 RELATED ID: 2Y2C RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AMPD APOENZYME REMARK 900 RELATED ID: 2Y2D RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AMPD HOLOENZYME REMARK 900 RELATED ID: 2Y2E RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AMPD GROWN AT PH 5.5 REMARK 900 RELATED ID: 2Y28 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SE-MET AMPD DERIVATIVE DBREF 2Y2B A 1 187 UNP P82974 AMPD_CITFR 1 187 DBREF 2Y2B B 1 187 UNP P82974 AMPD_CITFR 1 187 DBREF 2Y2B C 1 187 UNP P82974 AMPD_CITFR 1 187 SEQRES 1 A 187 MET LEU LEU ASP GLU GLY TRP LEU ALA GLU ALA ARG ARG SEQRES 2 A 187 VAL PRO SER PRO HIS TYR ASP CYS ARG PRO ASP ASP GLU SEQRES 3 A 187 ASN PRO SER LEU LEU VAL VAL HIS ASN ILE SER LEU PRO SEQRES 4 A 187 PRO GLY GLU PHE GLY GLY PRO TRP ILE ASP ALA LEU PHE SEQRES 5 A 187 THR GLY THR ILE ASP PRO ASN ALA HIS PRO TYR PHE ALA SEQRES 6 A 187 GLY ILE ALA HIS LEU ARG VAL SER ALA HIS CYS LEU ILE SEQRES 7 A 187 ARG ARG ASP GLY GLU ILE VAL GLN TYR VAL PRO PHE ASP SEQRES 8 A 187 LYS ARG ALA TRP HIS ALA GLY VAL SER SER TYR GLN GLY SEQRES 9 A 187 ARG GLU ARG CYS ASN ASP PHE SER ILE GLY ILE GLU LEU SEQRES 10 A 187 GLU GLY THR ASP THR LEU ALA TYR THR ASP ALA GLN TYR SEQRES 11 A 187 GLN GLN LEU ALA ALA VAL THR ASN ALA LEU ILE THR ARG SEQRES 12 A 187 TYR PRO ALA ILE ALA ASN ASN MET THR GLY HIS CYS ASN SEQRES 13 A 187 ILE ALA PRO GLU ARG LYS THR ASP PRO GLY PRO SER PHE SEQRES 14 A 187 ASP TRP ALA ARG PHE ARG ALA LEU VAL THR PRO SER SER SEQRES 15 A 187 HIS LYS GLU MET THR SEQRES 1 B 187 MET LEU LEU ASP GLU GLY TRP LEU ALA GLU ALA ARG ARG SEQRES 2 B 187 VAL PRO SER PRO HIS TYR ASP CYS ARG PRO ASP ASP GLU SEQRES 3 B 187 ASN PRO SER LEU LEU VAL VAL HIS ASN ILE SER LEU PRO SEQRES 4 B 187 PRO GLY GLU PHE GLY GLY PRO TRP ILE ASP ALA LEU PHE SEQRES 5 B 187 THR GLY THR ILE ASP PRO ASN ALA HIS PRO TYR PHE ALA SEQRES 6 B 187 GLY ILE ALA HIS LEU ARG VAL SER ALA HIS CYS LEU ILE SEQRES 7 B 187 ARG ARG ASP GLY GLU ILE VAL GLN TYR VAL PRO PHE ASP SEQRES 8 B 187 LYS ARG ALA TRP HIS ALA GLY VAL SER SER TYR GLN GLY SEQRES 9 B 187 ARG GLU ARG CYS ASN ASP PHE SER ILE GLY ILE GLU LEU SEQRES 10 B 187 GLU GLY THR ASP THR LEU ALA TYR THR ASP ALA GLN TYR SEQRES 11 B 187 GLN GLN LEU ALA ALA VAL THR ASN ALA LEU ILE THR ARG SEQRES 12 B 187 TYR PRO ALA ILE ALA ASN ASN MET THR GLY HIS CYS ASN SEQRES 13 B 187 ILE ALA PRO GLU ARG LYS THR ASP PRO GLY PRO SER PHE SEQRES 14 B 187 ASP TRP ALA ARG PHE ARG ALA LEU VAL THR PRO SER SER SEQRES 15 B 187 HIS LYS GLU MET THR SEQRES 1 C 187 MET LEU LEU ASP GLU GLY TRP LEU ALA GLU ALA ARG ARG SEQRES 2 C 187 VAL PRO SER PRO HIS TYR ASP CYS ARG PRO ASP ASP GLU SEQRES 3 C 187 ASN PRO SER LEU LEU VAL VAL HIS ASN ILE SER LEU PRO SEQRES 4 C 187 PRO GLY GLU PHE GLY GLY PRO TRP ILE ASP ALA LEU PHE SEQRES 5 C 187 THR GLY THR ILE ASP PRO ASN ALA HIS PRO TYR PHE ALA SEQRES 6 C 187 GLY ILE ALA HIS LEU ARG VAL SER ALA HIS CYS LEU ILE SEQRES 7 C 187 ARG ARG ASP GLY GLU ILE VAL GLN TYR VAL PRO PHE ASP SEQRES 8 C 187 LYS ARG ALA TRP HIS ALA GLY VAL SER SER TYR GLN GLY SEQRES 9 C 187 ARG GLU ARG CYS ASN ASP PHE SER ILE GLY ILE GLU LEU SEQRES 10 C 187 GLU GLY THR ASP THR LEU ALA TYR THR ASP ALA GLN TYR SEQRES 11 C 187 GLN GLN LEU ALA ALA VAL THR ASN ALA LEU ILE THR ARG SEQRES 12 C 187 TYR PRO ALA ILE ALA ASN ASN MET THR GLY HIS CYS ASN SEQRES 13 C 187 ILE ALA PRO GLU ARG LYS THR ASP PRO GLY PRO SER PHE SEQRES 14 C 187 ASP TRP ALA ARG PHE ARG ALA LEU VAL THR PRO SER SER SEQRES 15 C 187 HIS LYS GLU MET THR HET AH0 A 201 19 HET MHI A 202 27 HET ZN A 203 1 HET ZN B 201 1 HET ZN C 201 1 HETNAM AH0 2-(2-ACETYLAMINO-4-HYDROXY-6,8-DIOXA-BICYCLO[3.2.1]OCT- HETNAM 2 AH0 3-YLOXY)-PROPIONIC ACID HETNAM MHI L-ALA-GAMMA-D-GLU-MESO-DIAMINOPIMELIC ACID HETNAM ZN ZINC ION HETSYN AH0 1,6-ANHYDRO-N-ACETYLMURAMIC ACID FORMUL 4 AH0 C11 H17 N O7 FORMUL 5 MHI C15 H26 N4 O8 FORMUL 6 ZN 3(ZN 2+) FORMUL 9 HOH *556(H2 O) HELIX 1 1 PRO A 23 GLU A 26 5 4 HELIX 2 2 PRO A 46 THR A 53 1 8 HELIX 3 3 HIS A 61 HIS A 69 1 9 HELIX 4 4 CYS A 108 ASP A 110 5 3 HELIX 5 5 THR A 126 TYR A 144 1 19 HELIX 6 6 PRO A 145 ASN A 149 5 5 HELIX 7 7 HIS A 154 ALA A 158 1 5 HELIX 8 8 ASP A 170 VAL A 178 1 9 HELIX 9 9 PRO B 23 GLU B 26 5 4 HELIX 10 10 PRO B 46 THR B 53 1 8 HELIX 11 11 HIS B 61 ALA B 68 1 8 HELIX 12 12 CYS B 108 ASP B 110 5 3 HELIX 13 13 THR B 126 TYR B 144 1 19 HELIX 14 14 PRO B 145 ASN B 149 5 5 HELIX 15 15 HIS B 154 ALA B 158 1 5 HELIX 16 16 ASP B 170 VAL B 178 1 9 HELIX 17 17 ARG C 22 GLU C 26 5 5 HELIX 18 18 PRO C 46 GLY C 54 1 9 HELIX 19 19 HIS C 61 ALA C 68 1 8 HELIX 20 20 CYS C 108 ASP C 110 5 3 HELIX 21 21 THR C 126 TYR C 144 1 19 HELIX 22 22 PRO C 145 ASN C 149 5 5 HELIX 23 23 HIS C 154 ALA C 158 1 5 HELIX 24 24 ASP C 170 ALA C 176 1 7 SHEET 1 AA 2 LEU A 3 ASP A 4 0 SHEET 2 AA 2 TRP A 7 LEU A 8 -1 O TRP A 7 N ASP A 4 SHEET 1 AB 6 ARG A 12 ARG A 13 0 SHEET 2 AB 6 ILE A 84 GLN A 86 1 O ILE A 84 N ARG A 12 SHEET 3 AB 6 CYS A 76 ILE A 78 -1 O LEU A 77 N VAL A 85 SHEET 4 AB 6 SER A 112 GLU A 118 1 O GLU A 116 N ILE A 78 SHEET 5 AB 6 LEU A 30 ILE A 36 1 O LEU A 30 N ILE A 113 SHEET 6 AB 6 MET A 151 GLY A 153 1 O THR A 152 N VAL A 33 SHEET 1 AC 2 TYR A 19 CYS A 21 0 SHEET 2 AC 2 LYS A 92 ALA A 94 -1 O ARG A 93 N ASP A 20 SHEET 1 AD 2 SER A 101 TYR A 102 0 SHEET 2 AD 2 ARG A 105 GLU A 106 -1 O ARG A 105 N TYR A 102 SHEET 1 BA 2 LEU B 3 ASP B 4 0 SHEET 2 BA 2 TRP B 7 LEU B 8 -1 O TRP B 7 N ASP B 4 SHEET 1 BB 6 ARG B 12 ARG B 13 0 SHEET 2 BB 6 ILE B 84 GLN B 86 1 O ILE B 84 N ARG B 12 SHEET 3 BB 6 CYS B 76 ILE B 78 -1 O LEU B 77 N VAL B 85 SHEET 4 BB 6 SER B 112 GLU B 118 1 O GLY B 114 N CYS B 76 SHEET 5 BB 6 LEU B 30 ILE B 36 1 O LEU B 30 N ILE B 113 SHEET 6 BB 6 MET B 151 GLY B 153 1 O THR B 152 N VAL B 33 SHEET 1 BC 2 TYR B 19 CYS B 21 0 SHEET 2 BC 2 LYS B 92 ALA B 94 -1 O ARG B 93 N ASP B 20 SHEET 1 BD 2 SER B 101 TYR B 102 0 SHEET 2 BD 2 ARG B 105 GLU B 106 -1 O ARG B 105 N TYR B 102 SHEET 1 CA 2 LEU C 3 ASP C 4 0 SHEET 2 CA 2 TRP C 7 LEU C 8 -1 O TRP C 7 N ASP C 4 SHEET 1 CB 6 ARG C 12 ARG C 13 0 SHEET 2 CB 6 ILE C 84 GLN C 86 1 O ILE C 84 N ARG C 12 SHEET 3 CB 6 CYS C 76 ILE C 78 -1 O LEU C 77 N VAL C 85 SHEET 4 CB 6 SER C 112 GLU C 118 1 O GLY C 114 N CYS C 76 SHEET 5 CB 6 LEU C 30 ILE C 36 1 O LEU C 30 N ILE C 113 SHEET 6 CB 6 MET C 151 GLY C 153 1 O THR C 152 N VAL C 33 SHEET 1 CC 2 TYR C 19 ASP C 20 0 SHEET 2 CC 2 ARG C 93 ALA C 94 -1 O ARG C 93 N ASP C 20 SHEET 1 CD 2 SER C 101 TYR C 102 0 SHEET 2 CD 2 ARG C 105 GLU C 106 -1 O ARG C 105 N TYR C 102 LINK ND1 HIS A 34 ZN ZN A 203 1555 1555 2.04 LINK ND1 HIS A 154 ZN ZN A 203 1555 1555 2.05 LINK OD1 ASP A 164 ZN ZN A 203 1555 1555 2.47 LINK OD2 ASP A 164 ZN ZN A 203 1555 1555 1.96 LINK O AH0 A 201 ZN ZN A 203 1555 1555 2.66 LINK OXT AH0 A 201 ZN ZN A 203 1555 1555 2.25 LINK ND1 HIS B 34 ZN ZN B 201 1555 1555 2.07 LINK ND1 HIS B 154 ZN ZN B 201 1555 1555 2.03 LINK OD2 ASP B 164 ZN ZN B 201 1555 1555 1.96 LINK OD1 ASP B 164 ZN ZN B 201 1555 1555 2.47 LINK ZN ZN B 201 O HOH B 450 1555 1555 2.16 LINK ND1 HIS C 34 ZN ZN C 201 1555 1555 2.06 LINK ND1 HIS C 154 ZN ZN C 201 1555 1555 2.03 LINK OD1 ASP C 164 ZN ZN C 201 1555 1555 2.39 LINK OD2 ASP C 164 ZN ZN C 201 1555 1555 2.00 LINK ZN ZN C 201 O HOH C 430 1555 1555 2.22 CISPEP 1 LEU A 38 PRO A 39 0 -10.60 CISPEP 2 ASP A 164 PRO A 165 0 4.63 CISPEP 3 LEU B 38 PRO B 39 0 -9.87 CISPEP 4 ASP B 164 PRO B 165 0 6.15 CISPEP 5 LEU C 38 PRO C 39 0 -6.06 CISPEP 6 ASP C 164 PRO C 165 0 2.27 SITE 1 AC1 13 HIS A 34 ASN A 35 ILE A 36 LEU A 38 SITE 2 AC1 13 LEU A 51 TYR A 63 ILE A 67 GLU A 116 SITE 3 AC1 13 HIS A 154 LYS A 162 ASP A 164 MHI A 202 SITE 4 AC1 13 ZN A 203 SITE 1 AC2 20 HIS A 34 PHE A 52 ARG A 71 VAL A 72 SITE 2 AC2 20 SER A 73 TRP A 95 HIS A 96 ALA A 97 SITE 3 AC2 20 GLY A 98 ARG A 107 ASN A 109 GLU A 116 SITE 4 AC2 20 HIS A 154 ARG A 161 ARG A 175 AH0 A 201 SITE 5 AC2 20 ZN A 203 HOH A 414 HOH A 424 HOH A 311 SITE 1 AC3 5 HIS A 34 HIS A 154 ASP A 164 AH0 A 201 SITE 2 AC3 5 MHI A 202 SITE 1 AC4 4 HIS B 34 HIS B 154 ASP B 164 HOH B 450 SITE 1 AC5 4 HIS C 34 HIS C 154 ASP C 164 HOH C 430 CRYST1 67.774 67.774 92.836 90.00 90.00 120.00 P 32 9 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 0.014755 0.008519 0.000000 0.00000 SCALE2 0.000000 0.017038 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010772 0.00000