PDB Short entry for 2Y2D HEADER HYDROLASE 14-DEC-10 2Y2D TITLE CRYSTAL STRUCTURE OF AMPD HOLOENZYME 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 2 14-SEP-11 2Y2D 1 JRNL REVDAT 1 20-JUL-11 2Y2D 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. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT 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) : 2.000 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 9.997 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.07 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.21 REMARK 3 NUMBER OF REFLECTIONS : 31624 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.2108 REMARK 3 R VALUE (WORKING SET) : 0.2055 REMARK 3 FREE R VALUE : 0.2783 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.2 REMARK 3 FREE R VALUE TEST SET COUNT : 2272 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 9.9974 - 4.2104 1.00 2952 227 0.2274 0.2494 REMARK 3 2 4.2104 - 3.3845 1.00 2981 199 0.1821 0.2432 REMARK 3 3 3.3845 - 2.9695 1.00 2997 218 0.1839 0.2440 REMARK 3 4 2.9695 - 2.7039 1.00 2953 219 0.2010 0.2865 REMARK 3 5 2.7039 - 2.5134 1.00 2962 222 0.2042 0.2725 REMARK 3 6 2.5134 - 2.3672 1.00 2972 222 0.1980 0.3012 REMARK 3 7 2.3672 - 2.2501 0.99 2872 244 0.2062 0.3034 REMARK 3 8 2.2501 - 2.1532 0.99 2942 245 0.2164 0.3293 REMARK 3 9 2.1532 - 2.0710 0.98 2876 245 0.2192 0.3153 REMARK 3 10 2.0710 - 2.0002 0.97 2845 231 0.2216 0.3014 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 : 0.553 REMARK 3 B_SOL : 99 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.35 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.47 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.05 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.1123 REMARK 3 B22 (A**2) : 2.1123 REMARK 3 B33 (A**2) : -4.2247 REMARK 3 B12 (A**2) : 0.0000 REMARK 3 B13 (A**2) : 0.0000 REMARK 3 B23 (A**2) : 0.0000 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 4365 REMARK 3 ANGLE : 1.195 5976 REMARK 3 CHIRALITY : 0.078 630 REMARK 3 PLANARITY : 0.006 795 REMARK 3 DIHEDRAL : 18.271 1542 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 2Y2D 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 PDBE ID CODE IS EBI-46737. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-10 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) : 0.97625 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD (QUANTUM 315R) REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32155 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.00 REMARK 200 RESOLUTION RANGE LOW (A) : 35.80 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.4 REMARK 200 R MERGE (I) : 0.11 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.00 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) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.2 REMARK 200 R MERGE FOR SHELL (I) : 0.48 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.60 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 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 6.0, 0.1 M LI2SO4, REMARK 280 28% PEG 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 61.87000 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 30.93500 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 PRO B 180 REMARK 465 SER B 181 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 PRO C 180 REMARK 465 SER C 181 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: 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 ILE B 113 O HOH B 2252 2.11 REMARK 500 O SER C 37 O HOH C 2111 2.12 REMARK 500 O VAL C 136 O HOH C 2222 2.14 REMARK 500 O ILE B 56 O HOH B 2172 2.16 REMARK 500 O HOH A 2129 O HOH A 2230 2.17 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 167 C - N - CA ANGL. DEV. = 9.1 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 GLU A 5 69.11 30.23 REMARK 500 SER A 29 -61.77 -126.10 REMARK 500 ILE A 56 150.42 -47.19 REMARK 500 PRO A 58 -7.83 -53.71 REMARK 500 HIS A 61 135.82 178.03 REMARK 500 ALA A 68 22.60 -68.39 REMARK 500 VAL A 99 90.20 -66.82 REMARK 500 GLN A 103 72.54 52.12 REMARK 500 ALA A 158 55.09 -148.98 REMARK 500 GLU A 160 -67.58 69.31 REMARK 500 ALA A 176 -14.11 -49.05 REMARK 500 GLU B 5 72.00 53.99 REMARK 500 LEU B 8 107.63 -45.48 REMARK 500 ALA B 11 144.79 -39.09 REMARK 500 ASP B 20 -158.35 -132.31 REMARK 500 ILE B 36 144.08 -172.51 REMARK 500 TRP B 95 63.94 -116.25 REMARK 500 TYR B 144 75.56 -113.80 REMARK 500 ARG B 161 -35.83 -148.75 REMARK 500 VAL C 14 70.49 -116.75 REMARK 500 ASP C 25 27.14 46.72 REMARK 500 TRP C 95 71.40 -116.09 REMARK 500 ALA C 146 -2.46 -59.60 REMARK 500 GLU C 160 -48.47 67.18 REMARK 500 REMARK 500 REMARK: NULL 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 A1180 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 34 ND1 REMARK 620 2 HIS A 154 ND1 99.9 REMARK 620 3 ASP A 164 OD1 168.4 84.4 REMARK 620 4 ASP A 164 OD2 106.3 119.2 62.5 REMARK 620 5 HOH A2273 O 87.8 89.1 103.1 144.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1180 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 34 ND1 REMARK 620 2 HOH B2314 O 100.6 REMARK 620 3 HIS B 154 ND1 97.7 107.8 REMARK 620 4 ASP B 164 OD1 145.7 112.1 82.5 REMARK 620 5 ASP B 164 OD2 100.7 110.8 132.9 58.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C1180 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP C 164 OD1 REMARK 620 2 ASP C 164 OD2 60.3 REMARK 620 3 HOH C2276 O 107.5 124.7 REMARK 620 4 HIS C 154 ND1 82.0 127.6 99.4 REMARK 620 5 HIS C 34 ND1 147.2 97.1 104.9 97.2 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1180 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B1180 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C1180 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: 2Y2E RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AMPD GROWN AT PH 5.5 REMARK 900 RELATED ID: 2Y2C RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AMPD APOENZYME REMARK 900 RELATED ID: 2Y28 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SE-MET AMPD DERIVATIVE REMARK 900 RELATED ID: 2Y2B RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AMPD IN COMPLEX WITH REMARK 900 REACTION PRODUCTS DBREF 2Y2D A 1 187 UNP P82974 AMPD_CITFR 1 187 DBREF 2Y2D B 1 187 UNP P82974 AMPD_CITFR 1 187 DBREF 2Y2D 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 ZN A1180 1 HET ZN B1180 1 HET ZN C1180 1 HETNAM ZN ZINC ION FORMUL 4 ZN 3(ZN 2+) FORMUL 5 HOH *863(H2 O) HELIX 1 1 ARG A 22 GLU A 26 5 5 HELIX 2 2 PRO A 46 PHE A 52 1 7 HELIX 3 3 THR A 126 TYR A 144 1 19 HELIX 4 4 PRO A 145 ASN A 149 5 5 HELIX 5 5 HIS A 154 ALA A 158 1 5 HELIX 6 6 ASP A 170 ALA A 176 1 7 HELIX 7 7 PRO B 23 GLU B 26 5 4 HELIX 8 8 PRO B 46 PHE B 52 1 7 HELIX 9 9 HIS B 61 ALA B 68 1 8 HELIX 10 10 CYS B 108 ASP B 110 5 3 HELIX 11 11 THR B 126 TYR B 144 1 19 HELIX 12 12 PRO B 145 ASN B 149 5 5 HELIX 13 13 HIS B 154 ALA B 158 1 5 HELIX 14 14 ASP B 170 VAL B 178 1 9 HELIX 15 15 ARG C 22 GLU C 26 5 5 HELIX 16 16 PRO C 46 GLY C 54 1 9 HELIX 17 17 TYR C 63 ALA C 68 1 6 HELIX 18 18 CYS C 108 ASP C 110 5 3 HELIX 19 19 THR C 126 TYR C 144 1 19 HELIX 20 20 PRO C 145 ASN C 149 5 5 HELIX 21 21 HIS C 154 ALA C 158 1 5 HELIX 22 22 ASP C 170 LEU C 177 1 8 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 GLY A 114 N CYS A 76 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 ASP A 20 0 SHEET 2 AC 2 ARG A 93 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 6 ARG B 12 ARG B 13 0 SHEET 2 BA 6 ILE B 84 GLN B 86 1 O ILE B 84 N ARG B 12 SHEET 3 BA 6 CYS B 76 ILE B 78 -1 O LEU B 77 N VAL B 85 SHEET 4 BA 6 SER B 112 GLU B 118 1 O GLU B 116 N ILE B 78 SHEET 5 BA 6 LEU B 30 ILE B 36 1 O LEU B 30 N ILE B 113 SHEET 6 BA 6 MET B 151 GLY B 153 1 O THR B 152 N VAL B 33 SHEET 1 BB 2 ASP B 20 CYS B 21 0 SHEET 2 BB 2 LYS B 92 ARG B 93 -1 O ARG B 93 N ASP B 20 SHEET 1 BC 2 SER B 101 TYR B 102 0 SHEET 2 BC 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 GLU C 116 N ILE C 78 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 SER C 101 TYR C 102 0 SHEET 2 CC 2 ARG C 105 GLU C 106 -1 O ARG C 105 N TYR C 102 LINK ZN ZN A1180 ND1 HIS A 34 1555 1555 2.02 LINK ZN ZN A1180 ND1 HIS A 154 1555 1555 2.07 LINK ZN ZN A1180 OD1 ASP A 164 1555 1555 2.09 LINK ZN ZN A1180 OD2 ASP A 164 1555 1555 2.10 LINK ZN ZN A1180 O HOH A2273 1555 1555 2.27 LINK ZN ZN B1180 ND1 HIS B 34 1555 1555 2.06 LINK ZN ZN B1180 O HOH B2314 1555 1555 2.21 LINK ZN ZN B1180 ND1 HIS B 154 1555 1555 1.98 LINK ZN ZN B1180 OD1 ASP B 164 1555 1555 2.32 LINK ZN ZN B1180 OD2 ASP B 164 1555 1555 2.03 LINK ZN ZN C1180 OD2 ASP C 164 1555 1555 2.01 LINK ZN ZN C1180 O HOH C2276 1555 1555 2.19 LINK ZN ZN C1180 ND1 HIS C 154 1555 1555 2.04 LINK ZN ZN C1180 ND1 HIS C 34 1555 1555 2.00 LINK ZN ZN C1180 OD1 ASP C 164 1555 1555 2.24 CISPEP 1 LEU A 38 PRO A 39 0 -4.04 CISPEP 2 ASP A 164 PRO A 165 0 4.87 CISPEP 3 LEU B 38 PRO B 39 0 -5.18 CISPEP 4 ASP B 164 PRO B 165 0 2.57 CISPEP 5 LEU C 38 PRO C 39 0 -8.44 CISPEP 6 ASP C 164 PRO C 165 0 3.10 SITE 1 AC1 4 HIS A 34 HIS A 154 ASP A 164 HOH A2273 SITE 1 AC2 4 HIS B 34 HIS B 154 ASP B 164 HOH B2314 SITE 1 AC3 4 HIS C 34 HIS C 154 ASP C 164 HOH C2276 CRYST1 67.691 67.691 92.805 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 0.014773 0.008529 0.000000 0.00000 SCALE2 0.000000 0.017058 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010775 0.00000