HEADER HYDROLASE 10-FEB-06 2DEA TITLE CRYSTAL STRUCTURE OF THE AMINOPEPTIDASE OF AEROMONAS PROTEOLYTICA AT TITLE 2 PH 4.7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BACTERIAL LEUCYL AMINOPEPTIDASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.11.10; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO PROTEOLYTICUS; SOURCE 3 ORGANISM_TAXID: 671; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS AMINOPEPTIDASE, METALLOENZYME, BIMETALLOENZYME, LOW PH, ZINC ENZYME, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR G.A.PETSKO,D.RINGE,W.DESMARAIS REVDAT 3 30-OCT-24 2DEA 1 REMARK LINK REVDAT 2 24-FEB-09 2DEA 1 VERSN REVDAT 1 25-JUL-06 2DEA 0 JRNL AUTH W.DESMARAIS,D.L.BIENVENUE,K.P.BZYMEK,G.A.PETSKO,D.RINGE, JRNL AUTH 2 R.C.HOLZ JRNL TITL THE HIGH-RESOLUTION STRUCTURES OF THE NEUTRAL AND THE LOW PH JRNL TITL 2 CRYSTALS OF AMINOPEPTIDASE FROM AEROMONAS PROTEOLYTICA. JRNL REF J.BIOL.INORG.CHEM. V. 11 398 2006 JRNL REFN ISSN 0949-8257 JRNL PMID 16596389 JRNL DOI 10.1007/S00775-006-0093-X REMARK 2 REMARK 2 RESOLUTION. 1.24 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.24 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.153 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.163 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 81189 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2210 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 393 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 ANGLE DISTANCES (A) : NULL REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DEA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-FEB-06. REMARK 100 THE DEPOSITION ID IS D_1000025315. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAR-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : DIAMOND REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 81189 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.240 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.24 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 65.8 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NAACETATE, KSCN, NACL, PH 4.7, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 30.27200 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 60.54400 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 45.40800 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 75.68000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 15.13600 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 30.27200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 60.54400 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 75.68000 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 45.40800 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 15.13600 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 532 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 588 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 705 LIES ON A SPECIAL POSITION. 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 ASP A 292 REMARK 465 THR A 293 REMARK 465 PRO A 294 REMARK 465 THR A 295 REMARK 465 PRO A 296 REMARK 465 GLY A 297 REMARK 465 ASN A 298 REMARK 465 GLN A 299 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 SER A 20 OG REMARK 480 SER A 27 OG REMARK 480 SER A 31 OG REMARK 480 SER A 41 OG REMARK 480 GLN A 44 CG CD OE1 NE2 REMARK 480 LEU A 56 CG CD1 CD2 REMARK 480 SER A 64 OG REMARK 480 SER A 71 N CA C O CB OG REMARK 480 LYS A 140 NZ REMARK 480 GLN A 164 CD OE1 NE2 REMARK 480 LEU A 176 CG CD1 CD2 REMARK 480 MET A 209 SD CE REMARK 480 LYS A 247 CE NZ REMARK 480 SER A 265 OG REMARK 480 SER A 270 OG REMARK 480 LYS A 274 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 OE1 GLN A 44 O HOH A 770 0.39 REMARK 500 NE2 GLN A 164 O HOH A 854 0.89 REMARK 500 CD GLN A 44 O HOH A 770 1.00 REMARK 500 CD GLN A 164 O HOH A 854 1.49 REMARK 500 NE2 GLN A 164 O HOH A 676 1.90 REMARK 500 NE2 GLN A 44 O HOH A 770 1.92 REMARK 500 OE1 GLN A 164 O HOH A 854 2.00 REMARK 500 OG SER A 57 O HOH A 865 2.03 REMARK 500 NE2 GLN A 44 O HOH A 823 2.19 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 SER A 57 CA SER A 57 CB 0.095 REMARK 500 SER A 59 C LEU A 60 N -0.214 REMARK 500 GLY A 291 C GLY A 291 O 1.560 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 ASP A 89 CB - CG - OD1 ANGL. DEV. = 10.4 DEGREES REMARK 500 ASP A 89 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ARG A 156 NE - CZ - NH1 ANGL. DEV. = 7.7 DEGREES REMARK 500 ARG A 156 NE - CZ - NH2 ANGL. DEV. = -12.9 DEGREES REMARK 500 TYR A 165 CB - CG - CD2 ANGL. DEV. = 4.2 DEGREES REMARK 500 PHE A 201 CB - CG - CD1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ASP A 210 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 TYR A 251 CB - CG - CD1 ANGL. DEV. = 5.3 DEGREES REMARK 500 TYR A 251 CG - CD1 - CE1 ANGL. DEV. = 6.3 DEGREES REMARK 500 THR A 290 O - C - N ANGL. DEV. = 12.2 DEGREES REMARK 500 GLY A 291 CA - C - O ANGL. DEV. = -34.7 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 86 -33.07 -132.40 REMARK 500 MET A 180 98.41 76.44 REMARK 500 SER A 265 -142.99 -98.91 REMARK 500 THR A 290 -3.45 -144.04 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 SER A 57 ALA A 58 -149.18 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 A 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 97 NE2 REMARK 620 2 ASP A 117 OD1 94.6 REMARK 620 3 ASP A 179 OD1 98.0 92.2 REMARK 620 4 ASP A 179 OD2 90.6 153.3 61.1 REMARK 620 5 HOH A 640 O 107.8 100.4 150.1 102.9 REMARK 620 6 HOH A 797 O 173.9 88.5 87.2 89.0 66.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 117 OD2 REMARK 620 2 GLU A 152 OE2 94.7 REMARK 620 3 GLU A 152 OE1 149.8 55.3 REMARK 620 4 HIS A 256 NE2 93.8 103.8 89.9 REMARK 620 5 HOH A 640 O 97.9 91.9 88.4 159.5 REMARK 620 6 HOH A 644 O 101.4 156.8 108.5 91.7 69.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 218 OH REMARK 620 2 HOH A 534 O 99.1 REMARK 620 3 HOH A 538 O 79.9 89.2 REMARK 620 4 HOH A 545 O 176.3 82.5 103.5 REMARK 620 5 HOH A 548 O 78.3 171.8 82.7 100.6 REMARK 620 6 HOH A 550 O 85.6 95.7 165.3 90.9 91.8 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 ZN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LOK RELATED DB: PDB REMARK 900 RELATED ID: 1RTQ RELATED DB: PDB REMARK 900 RELATED ID: 1FT7 RELATED DB: PDB REMARK 900 RELATED ID: 1TXR RELATED DB: PDB DBREF 2DEA A 1 299 UNP Q01693 AMPX_VIBPR 107 405 SEQRES 1 A 299 MET PRO PRO ILE THR GLN GLN ALA THR VAL THR ALA TRP SEQRES 2 A 299 LEU PRO GLN VAL ASP ALA SER GLN ILE THR GLY THR ILE SEQRES 3 A 299 SER SER LEU GLU SER PHE THR ASN ARG PHE TYR THR THR SEQRES 4 A 299 THR SER GLY ALA GLN ALA SER ASP TRP ILE ALA SER GLU SEQRES 5 A 299 TRP GLN ALA LEU SER ALA SER LEU PRO ASN ALA SER VAL SEQRES 6 A 299 LYS GLN VAL SER HIS SER GLY TYR ASN GLN LYS SER VAL SEQRES 7 A 299 VAL MET THR ILE THR GLY SER GLU ALA PRO ASP GLU TRP SEQRES 8 A 299 ILE VAL ILE GLY GLY HIS LEU ASP SER THR ILE GLY SER SEQRES 9 A 299 HIS THR ASN GLU GLN SER VAL ALA PRO GLY ALA ASP ASP SEQRES 10 A 299 ASP ALA SER GLY ILE ALA ALA VAL THR GLU VAL ILE ARG SEQRES 11 A 299 VAL LEU SER GLU ASN ASN PHE GLN PRO LYS ARG SER ILE SEQRES 12 A 299 ALA PHE MET ALA TYR ALA ALA GLU GLU VAL GLY LEU ARG SEQRES 13 A 299 GLY SER GLN ASP LEU ALA ASN GLN TYR LYS SER GLU GLY SEQRES 14 A 299 LYS ASN VAL VAL SER ALA LEU GLN LEU ASP MET THR ASN SEQRES 15 A 299 TYR LYS GLY SER ALA GLN ASP VAL VAL PHE ILE THR ASP SEQRES 16 A 299 TYR THR ASP SER ASN PHE THR GLN TYR LEU THR GLN LEU SEQRES 17 A 299 MET ASP GLU TYR LEU PRO SER LEU THR TYR GLY PHE ASP SEQRES 18 A 299 THR CYS GLY TYR ALA CYS SER ASP HIS ALA SER TRP HIS SEQRES 19 A 299 ASN ALA GLY TYR PRO ALA ALA MET PRO PHE GLU SER LYS SEQRES 20 A 299 PHE ASN ASP TYR ASN PRO ARG ILE HIS THR THR GLN ASP SEQRES 21 A 299 THR LEU ALA ASN SER ASP PRO THR GLY SER HIS ALA LYS SEQRES 22 A 299 LYS PHE THR GLN LEU GLY LEU ALA TYR ALA ILE GLU MET SEQRES 23 A 299 GLY SER ALA THR GLY ASP THR PRO THR PRO GLY ASN GLN HET ZN A 401 1 HET ZN A 402 1 HET NA A 403 1 HETNAM ZN ZINC ION HETNAM NA SODIUM ION FORMUL 2 ZN 2(ZN 2+) FORMUL 4 NA NA 1+ FORMUL 5 HOH *393(H2 O) HELIX 1 1 GLN A 6 LEU A 14 1 9 HELIX 2 2 PRO A 15 VAL A 17 5 3 HELIX 3 3 ASP A 18 SER A 31 1 14 HELIX 4 4 THR A 39 ALA A 58 1 20 HELIX 5 5 ASP A 118 ASN A 135 1 18 HELIX 6 6 ALA A 150 GLY A 154 5 5 HELIX 7 7 LEU A 155 GLU A 168 1 14 HELIX 8 8 ASP A 198 LEU A 213 1 16 HELIX 9 9 ASP A 229 ALA A 236 1 8 HELIX 10 10 LYS A 247 TYR A 251 5 5 HELIX 11 11 GLY A 269 ALA A 289 1 21 SHEET 1 A 8 ALA A 63 HIS A 70 0 SHEET 2 A 8 TYR A 73 ILE A 82 -1 O VAL A 79 N LYS A 66 SHEET 3 A 8 ARG A 141 TYR A 148 -1 O PHE A 145 N MET A 80 SHEET 4 A 8 ALA A 87 HIS A 97 1 N ILE A 92 O ALA A 144 SHEET 5 A 8 ASN A 171 GLN A 177 1 O ASN A 171 N TRP A 91 SHEET 6 A 8 ALA A 240 PHE A 244 1 O ALA A 241 N GLN A 177 SHEET 7 A 8 VAL A 190 ILE A 193 -1 N VAL A 191 O PHE A 244 SHEET 8 A 8 TYR A 218 ASP A 221 1 O GLY A 219 N PHE A 192 SSBOND 1 CYS A 223 CYS A 227 1555 1555 2.04 LINK NE2 HIS A 97 ZN ZN A 402 1555 1555 2.04 LINK OD2 ASP A 117 ZN ZN A 401 1555 1555 1.98 LINK OD1 ASP A 117 ZN ZN A 402 1555 1555 1.98 LINK OE2 GLU A 152 ZN ZN A 401 1555 1555 2.12 LINK OE1 GLU A 152 ZN ZN A 401 1555 1555 2.56 LINK OD1 ASP A 179 ZN ZN A 402 1555 1555 2.10 LINK OD2 ASP A 179 ZN ZN A 402 1555 1555 2.22 LINK OH TYR A 218 NA NA A 403 1555 1555 2.43 LINK NE2 HIS A 256 ZN ZN A 401 1555 1555 1.97 LINK ZN ZN A 401 O HOH A 640 1555 1555 2.19 LINK ZN ZN A 401 O HOH A 644 1555 1555 2.01 LINK ZN ZN A 402 O HOH A 640 1555 1555 1.92 LINK ZN ZN A 402 O HOH A 797 1555 1555 2.25 LINK NA NA A 403 O HOH A 534 1555 1555 2.43 LINK NA NA A 403 O HOH A 538 1555 1555 2.46 LINK NA NA A 403 O HOH A 545 1555 1555 2.36 LINK NA NA A 403 O HOH A 548 1555 1555 2.44 LINK NA NA A 403 O HOH A 550 1555 1555 2.35 CISPEP 1 ASP A 117 ASP A 118 0 0.73 SITE 1 AC1 6 ASP A 117 GLU A 152 HIS A 256 ZN A 402 SITE 2 AC1 6 HOH A 640 HOH A 644 SITE 1 AC2 6 HIS A 97 ASP A 117 ASP A 179 ZN A 401 SITE 2 AC2 6 HOH A 640 HOH A 797 SITE 1 AC3 6 TYR A 218 HOH A 534 HOH A 538 HOH A 545 SITE 2 AC3 6 HOH A 548 HOH A 550 CRYST1 109.605 109.605 90.816 90.00 90.00 120.00 P 61 2 2 12 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 0.009124 0.005268 0.000000 0.00000 SCALE2 0.000000 0.010535 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011011 0.00000