HEADER HYDROLASE 15-JAN-15 4XN9 TITLE CRYSTAL STRUCTURE OF E. COLI AMINOPEPTIDASE N IN COMPLEX WITH BETA TITLE 2 ALANINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMINOPEPTIDASE N; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 5-870; COMPND 5 SYNONYM: ALPHA-AMINOACYLPEPTIDE HYDROLASE; COMPND 6 EC: 3.4.11.2; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: PEPN, B0932, JW0915; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.ADDLAGATTA,R.GUMPENA REVDAT 2 08-NOV-23 4XN9 1 REMARK LINK REVDAT 1 02-MAR-16 4XN9 0 JRNL AUTH A.ADDLAGATTA,R.GUMPENA JRNL TITL CRYSTAL STRUCTURE OF E. COLI AMINOPEPTIDASE N IN COMPLEX JRNL TITL 2 WITH BETA ALANINE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.78 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 33989 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.137 REMARK 3 R VALUE (WORKING SET) : 0.134 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1784 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2432 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.65 REMARK 3 BIN R VALUE (WORKING SET) : 0.1820 REMARK 3 BIN FREE R VALUE SET COUNT : 133 REMARK 3 BIN FREE R VALUE : 0.2650 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6940 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 23 REMARK 3 SOLVENT ATOMS : 293 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.474 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.258 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.166 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.497 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7168 ; 0.016 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6750 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9740 ; 1.812 ; 1.951 REMARK 3 BOND ANGLES OTHERS (DEGREES): 15480 ; 0.886 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 879 ; 6.429 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 370 ;37.849 ;24.054 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1206 ;16.340 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 57 ;17.907 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1071 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8244 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1725 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3482 ; 2.197 ; 2.963 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3483 ; 2.197 ; 2.963 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4355 ; 3.453 ; 4.444 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4354 ; 3.453 ; 4.445 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3686 ; 3.359 ; 3.316 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3684 ; 3.356 ; 3.315 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5379 ; 5.309 ; 4.823 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 8241 ; 6.874 ;23.475 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 8186 ; 6.863 ;23.477 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4XN9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000205989. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : CU REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35916 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06000 REMARK 200 FOR THE DATA SET : 25.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.600 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: 2HPO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM MALONATE, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-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 56.79300 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 113.58600 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 113.58600 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 56.79300 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: 130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 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 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 HOH A 1236 O HOH A 1268 2.07 REMARK 500 NH2 ARG A 346 OE1 GLU A 615 2.11 REMARK 500 O HOH A 1001 O HOH A 1220 2.17 REMARK 500 O HOH A 1270 O HOH A 1284 2.19 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 24 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ARG A 126 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 222 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 582 NE - CZ - NH1 ANGL. DEV. = 8.0 DEGREES REMARK 500 ARG A 582 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 783 NE - CZ - NH1 ANGL. DEV. = 3.2 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 ASN A 67 49.28 34.48 REMARK 500 ALA A 73 78.99 -102.79 REMARK 500 GLU A 78 94.33 -49.00 REMARK 500 ASN A 169 32.91 70.18 REMARK 500 MET A 260 -168.51 -76.87 REMARK 500 GLU A 264 36.86 -78.59 REMARK 500 VAL A 276 -54.29 -130.77 REMARK 500 ASN A 306 -69.20 -100.89 REMARK 500 THR A 309 -166.21 -110.39 REMARK 500 ILE A 370 -60.87 -93.81 REMARK 500 PRO A 505 152.91 -45.78 REMARK 500 LEU A 589 132.63 -39.22 REMARK 500 ASN A 708 -58.53 109.21 REMARK 500 ALA A 758 173.51 -53.92 REMARK 500 ASN A 819 82.96 -159.71 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 A1293 DISTANCE = 6.72 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 NA A 904 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 19 OE1 REMARK 620 2 ILE A 20 O 87.2 REMARK 620 3 LEU A 138 O 125.2 81.8 REMARK 620 4 HOH A1187 O 87.2 153.4 80.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 901 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 297 NE2 REMARK 620 2 HIS A 301 NE2 104.2 REMARK 620 3 GLU A 320 OE1 110.1 105.0 REMARK 620 4 BAL A 902 OXT 116.3 125.0 94.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 903 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 332 O REMARK 620 2 ASP A 333 O 72.6 REMARK 620 3 GLY A 335 O 69.8 90.7 REMARK 620 4 HOH A1173 O 99.8 171.2 90.9 REMARK 620 5 HOH A1229 O 85.2 98.0 149.7 76.5 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 A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BAL A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MLI A 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MLI A 906 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4XMS RELATED DB: PDB REMARK 900 RELATED ID: 4XMT RELATED DB: PDB REMARK 900 RELATED ID: 4XMU RELATED DB: PDB REMARK 900 RELATED ID: 4XMV RELATED DB: PDB REMARK 900 RELATED ID: 4XMW RELATED DB: PDB REMARK 900 RELATED ID: 4XMX RELATED DB: PDB REMARK 900 RELATED ID: 4XMZ RELATED DB: PDB REMARK 900 RELATED ID: 4XN1 RELATED DB: PDB REMARK 900 RELATED ID: 4XN2 RELATED DB: PDB REMARK 900 RELATED ID: 4XN4 RELATED DB: PDB REMARK 900 RELATED ID: 4XN5 RELATED DB: PDB REMARK 900 RELATED ID: 4XN7 RELATED DB: PDB REMARK 900 RELATED ID: 4XN8 RELATED DB: PDB REMARK 900 RELATED ID: 4XNA RELATED DB: PDB REMARK 900 RELATED ID: 4XNB RELATED DB: PDB REMARK 900 RELATED ID: 4XND RELATED DB: PDB REMARK 900 RELATED ID: 4XO3 RELATED DB: PDB REMARK 900 RELATED ID: 4XO4 RELATED DB: PDB REMARK 900 RELATED ID: 4XO5 RELATED DB: PDB DBREF 4XN9 A 5 870 UNP P04825 AMPN_ECOLI 5 870 SEQRES 1 A 866 PRO GLN ALA LYS TYR ARG HIS ASP TYR ARG ALA PRO ASP SEQRES 2 A 866 TYR GLN ILE THR ASP ILE ASP LEU THR PHE ASP LEU ASP SEQRES 3 A 866 ALA GLN LYS THR VAL VAL THR ALA VAL SER GLN ALA VAL SEQRES 4 A 866 ARG HIS GLY ALA SER ASP ALA PRO LEU ARG LEU ASN GLY SEQRES 5 A 866 GLU ASP LEU LYS LEU VAL SER VAL HIS ILE ASN ASP GLU SEQRES 6 A 866 PRO TRP THR ALA TRP LYS GLU GLU GLU GLY ALA LEU VAL SEQRES 7 A 866 ILE SER ASN LEU PRO GLU ARG PHE THR LEU LYS ILE ILE SEQRES 8 A 866 ASN GLU ILE SER PRO ALA ALA ASN THR ALA LEU GLU GLY SEQRES 9 A 866 LEU TYR GLN SER GLY ASP ALA LEU CYS THR GLN CYS GLU SEQRES 10 A 866 ALA GLU GLY PHE ARG HIS ILE THR TYR TYR LEU ASP ARG SEQRES 11 A 866 PRO ASP VAL LEU ALA ARG PHE THR THR LYS ILE ILE ALA SEQRES 12 A 866 ASP LYS ILE LYS TYR PRO PHE LEU LEU SER ASN GLY ASN SEQRES 13 A 866 ARG VAL ALA GLN GLY GLU LEU GLU ASN GLY ARG HIS TRP SEQRES 14 A 866 VAL GLN TRP GLN ASP PRO PHE PRO LYS PRO CYS TYR LEU SEQRES 15 A 866 PHE ALA LEU VAL ALA GLY ASP PHE ASP VAL LEU ARG ASP SEQRES 16 A 866 THR PHE THR THR ARG SER GLY ARG GLU VAL ALA LEU GLU SEQRES 17 A 866 LEU TYR VAL ASP ARG GLY ASN LEU ASP ARG ALA PRO TRP SEQRES 18 A 866 ALA MET THR SER LEU LYS ASN SER MET LYS TRP ASP GLU SEQRES 19 A 866 GLU ARG PHE GLY LEU GLU TYR ASP LEU ASP ILE TYR MET SEQRES 20 A 866 ILE VAL ALA VAL ASP PHE PHE ASN MET GLY ALA MET GLU SEQRES 21 A 866 ASN LYS GLY LEU ASN ILE PHE ASN SER LYS TYR VAL LEU SEQRES 22 A 866 ALA ARG THR ASP THR ALA THR ASP LYS ASP TYR LEU ASP SEQRES 23 A 866 ILE GLU ARG VAL ILE GLY HIS GLU TYR PHE HIS ASN TRP SEQRES 24 A 866 THR GLY ASN ARG VAL THR CYS ARG ASP TRP PHE GLN LEU SEQRES 25 A 866 SER LEU LYS GLU GLY LEU THR VAL PHE ARG ASP GLN GLU SEQRES 26 A 866 PHE SER SER ASP LEU GLY SER ARG ALA VAL ASN ARG ILE SEQRES 27 A 866 ASN ASN VAL ARG THR MET ARG GLY LEU GLN PHE ALA GLU SEQRES 28 A 866 ASP ALA SER PRO MET ALA HIS PRO ILE ARG PRO ASP MET SEQRES 29 A 866 VAL ILE GLU MET ASN ASN PHE TYR THR LEU THR VAL TYR SEQRES 30 A 866 GLU LYS GLY ALA GLU VAL ILE ARG MET ILE HIS THR LEU SEQRES 31 A 866 LEU GLY GLU GLU ASN PHE GLN LYS GLY MET GLN LEU TYR SEQRES 32 A 866 PHE GLU ARG HIS ASP GLY SER ALA ALA THR CYS ASP ASP SEQRES 33 A 866 PHE VAL GLN ALA MET GLU ASP ALA SER ASN VAL ASP LEU SEQRES 34 A 866 SER HIS PHE ARG ARG TRP TYR SER GLN SER GLY THR PRO SEQRES 35 A 866 ILE VAL THR VAL LYS ASP ASP TYR ASN PRO GLU THR GLU SEQRES 36 A 866 GLN TYR THR LEU THR ILE SER GLN ARG THR PRO ALA THR SEQRES 37 A 866 PRO ASP GLN ALA GLU LYS GLN PRO LEU HIS ILE PRO PHE SEQRES 38 A 866 ALA ILE GLU LEU TYR ASP ASN GLU GLY LYS VAL ILE PRO SEQRES 39 A 866 LEU GLN LYS GLY GLY HIS PRO VAL ASN SER VAL LEU ASN SEQRES 40 A 866 VAL THR GLN ALA GLU GLN THR PHE VAL PHE ASP ASN VAL SEQRES 41 A 866 TYR PHE GLN PRO VAL PRO ALA LEU LEU CYS GLU PHE SER SEQRES 42 A 866 ALA PRO VAL LYS LEU GLU TYR LYS TRP SER ASP GLN GLN SEQRES 43 A 866 LEU THR PHE LEU MET ARG HIS ALA ARG ASN ASP PHE SER SEQRES 44 A 866 ARG TRP ASP ALA ALA GLN SER LEU LEU ALA THR TYR ILE SEQRES 45 A 866 LYS LEU ASN VAL ALA ARG HIS GLN GLN GLY GLN PRO LEU SEQRES 46 A 866 SER LEU PRO VAL HIS VAL ALA ASP ALA PHE ARG ALA VAL SEQRES 47 A 866 LEU LEU ASP GLU LYS ILE ASP PRO ALA LEU ALA ALA GLU SEQRES 48 A 866 ILE LEU THR LEU PRO SER VAL ASN GLU MET ALA GLU LEU SEQRES 49 A 866 PHE ASP ILE ILE ASP PRO ILE ALA ILE ALA GLU VAL ARG SEQRES 50 A 866 GLU ALA LEU THR ARG THR LEU ALA THR GLU LEU ALA ASP SEQRES 51 A 866 GLU LEU LEU ALA ILE TYR ASN ALA ASN TYR GLN SER GLU SEQRES 52 A 866 TYR ARG VAL GLU HIS GLU ASP ILE ALA LYS ARG THR LEU SEQRES 53 A 866 ARG ASN ALA CYS LEU ARG PHE LEU ALA PHE GLY GLU THR SEQRES 54 A 866 HIS LEU ALA ASP VAL LEU VAL SER LYS GLN PHE HIS GLU SEQRES 55 A 866 ALA ASN ASN MET THR ASP ALA LEU ALA ALA LEU SER ALA SEQRES 56 A 866 ALA VAL ALA ALA GLN LEU PRO CYS ARG ASP ALA LEU MET SEQRES 57 A 866 GLN GLU TYR ASP ASP LYS TRP HIS GLN ASN GLY LEU VAL SEQRES 58 A 866 MET ASP LYS TRP PHE ILE LEU GLN ALA THR SER PRO ALA SEQRES 59 A 866 ALA ASN VAL LEU GLU THR VAL ARG GLY LEU LEU GLN HIS SEQRES 60 A 866 ARG SER PHE THR MET SER ASN PRO ASN ARG ILE ARG SER SEQRES 61 A 866 LEU ILE GLY ALA PHE ALA GLY SER ASN PRO ALA ALA PHE SEQRES 62 A 866 HIS ALA GLU ASP GLY SER GLY TYR LEU PHE LEU VAL GLU SEQRES 63 A 866 MET LEU THR ASP LEU ASN SER ARG ASN PRO GLN VAL ALA SEQRES 64 A 866 SER ARG LEU ILE GLU PRO LEU ILE ARG LEU LYS ARG TYR SEQRES 65 A 866 ASP ALA LYS ARG GLN GLU LYS MET ARG ALA ALA LEU GLU SEQRES 66 A 866 GLN LEU LYS GLY LEU GLU ASN LEU SER GLY ASP LEU TYR SEQRES 67 A 866 GLU LYS ILE THR LYS ALA LEU ALA HET ZN A 901 1 HET BAL A 902 6 HET NA A 903 1 HET NA A 904 1 HET MLI A 905 7 HET MLI A 906 7 HETNAM ZN ZINC ION HETNAM BAL BETA-ALANINE HETNAM NA SODIUM ION HETNAM MLI MALONATE ION FORMUL 2 ZN ZN 2+ FORMUL 3 BAL C3 H7 N O2 FORMUL 4 NA 2(NA 1+) FORMUL 6 MLI 2(C3 H2 O4 2-) FORMUL 8 HOH *293(H2 O) HELIX 1 AA1 HIS A 11 TYR A 13 5 3 HELIX 2 AA2 SER A 99 ASN A 103 5 5 HELIX 3 AA3 GLY A 124 ILE A 128 5 5 HELIX 4 AA4 PRO A 183 PHE A 187 5 5 HELIX 5 AA5 ASN A 219 ARG A 222 5 4 HELIX 6 AA6 ALA A 223 GLY A 242 1 20 HELIX 7 AA7 LYS A 274 VAL A 276 5 3 HELIX 8 AA8 THR A 284 HIS A 301 1 18 HELIX 9 AA9 ASP A 312 PHE A 314 5 3 HELIX 10 AB1 GLN A 315 GLY A 335 1 21 HELIX 11 AB2 SER A 336 LEU A 351 1 16 HELIX 12 AB3 LEU A 351 ASP A 356 1 6 HELIX 13 AB4 GLU A 371 TYR A 376 5 6 HELIX 14 AB5 THR A 377 ASP A 412 1 36 HELIX 15 AB6 THR A 417 ASN A 430 1 14 HELIX 16 AB7 ARG A 437 GLN A 442 1 6 HELIX 17 AB8 SER A 547 ALA A 558 1 12 HELIX 18 AB9 ASN A 560 GLN A 585 1 26 HELIX 19 AC1 PRO A 592 LEU A 604 1 13 HELIX 20 AC2 ASP A 609 LEU A 617 1 9 HELIX 21 AC3 SER A 621 GLU A 627 1 7 HELIX 22 AC4 ASP A 633 LEU A 652 1 20 HELIX 23 AC5 LEU A 652 ASN A 663 1 12 HELIX 24 AC6 GLU A 671 PHE A 690 1 20 HELIX 25 AC7 GLU A 692 ALA A 707 1 16 HELIX 26 AC8 ASN A 709 ALA A 723 1 15 HELIX 27 AC9 CYS A 727 HIS A 740 1 14 HELIX 28 AD1 ASN A 742 THR A 755 1 14 HELIX 29 AD2 ASN A 760 LEU A 769 1 10 HELIX 30 AD3 ASN A 778 ASN A 793 1 16 HELIX 31 AD4 ASN A 793 HIS A 798 1 6 HELIX 32 AD5 GLY A 802 ASN A 819 1 18 HELIX 33 AD6 ASN A 819 GLU A 828 1 10 HELIX 34 AD7 PRO A 829 TYR A 836 5 8 HELIX 35 AD8 ASP A 837 GLY A 853 1 17 HELIX 36 AD9 SER A 858 ALA A 870 1 13 SHEET 1 AA1 2 LYS A 8 TYR A 9 0 SHEET 2 AA1 2 MET A 368 VAL A 369 -1 O VAL A 369 N LYS A 8 SHEET 1 AA2 8 GLU A 69 PRO A 70 0 SHEET 2 AA2 8 LYS A 60 ILE A 66 -1 N ILE A 66 O GLU A 69 SHEET 3 AA2 8 ARG A 89 ILE A 98 -1 O ILE A 95 N VAL A 62 SHEET 4 AA2 8 THR A 34 ARG A 44 -1 N VAL A 36 O ASN A 96 SHEET 5 AA2 8 TYR A 18 ASP A 28 -1 N THR A 26 O THR A 37 SHEET 6 AA2 8 ALA A 139 ASP A 148 1 O LYS A 144 N LEU A 25 SHEET 7 AA2 8 ARG A 171 LYS A 182 -1 O HIS A 172 N ALA A 147 SHEET 8 AA2 8 ASN A 160 LEU A 167 -1 N VAL A 162 O GLN A 175 SHEET 1 AA3 3 LEU A 52 ASN A 55 0 SHEET 2 AA3 3 ALA A 80 ILE A 83 -1 O LEU A 81 N LEU A 54 SHEET 3 AA3 3 TRP A 74 GLU A 77 -1 N LYS A 75 O VAL A 82 SHEET 1 AA4 4 GLY A 108 SER A 112 0 SHEET 2 AA4 4 ALA A 115 GLN A 119 -1 O GLN A 119 N GLY A 108 SHEET 3 AA4 4 LEU A 189 GLY A 192 -1 O ALA A 191 N LEU A 116 SHEET 4 AA4 4 PHE A 154 SER A 157 -1 N LEU A 156 O VAL A 190 SHEET 1 AA5 5 ASP A 195 THR A 202 0 SHEET 2 AA5 5 GLU A 208 VAL A 215 -1 O VAL A 209 N PHE A 201 SHEET 3 AA5 5 ILE A 249 VAL A 255 1 O ILE A 252 N TYR A 214 SHEET 4 AA5 5 LEU A 268 ASN A 272 1 O PHE A 271 N VAL A 253 SHEET 5 AA5 5 ALA A 262 MET A 263 -1 N MET A 263 O ILE A 270 SHEET 1 AA6 2 THR A 309 CYS A 310 0 SHEET 2 AA6 2 ALA A 415 ALA A 416 1 O ALA A 416 N THR A 309 SHEET 1 AA7 4 GLU A 516 PHE A 521 0 SHEET 2 AA7 4 GLN A 460 ARG A 468 -1 N LEU A 463 O PHE A 519 SHEET 3 AA7 4 ILE A 447 ASN A 455 -1 N LYS A 451 O THR A 464 SHEET 4 AA7 4 LYS A 541 GLU A 543 1 O LYS A 541 N VAL A 448 SHEET 1 AA8 2 ILE A 483 ALA A 486 0 SHEET 2 AA8 2 VAL A 509 VAL A 512 -1 O LEU A 510 N PHE A 485 SHEET 1 AA9 3 VAL A 496 ILE A 497 0 SHEET 2 AA9 3 GLU A 488 TYR A 490 -1 N LEU A 489 O ILE A 497 SHEET 3 AA9 3 VAL A 529 ALA A 531 -1 O ALA A 531 N GLU A 488 SHEET 1 AB1 2 GLN A 500 LYS A 501 0 SHEET 2 AB1 2 HIS A 504 PRO A 505 -1 O HIS A 504 N LYS A 501 LINK OE1 GLN A 19 NA NA A 904 1555 1555 2.30 LINK O ILE A 20 NA NA A 904 1555 1555 2.46 LINK O LEU A 138 NA NA A 904 1555 1555 2.49 LINK NE2 HIS A 297 ZN ZN A 901 1555 1555 2.10 LINK NE2 HIS A 301 ZN ZN A 901 1555 1555 2.08 LINK OE1 GLU A 320 ZN ZN A 901 1555 1555 2.17 LINK O SER A 332 NA NA A 903 1555 1555 2.63 LINK O ASP A 333 NA NA A 903 1555 1555 2.80 LINK O GLY A 335 NA NA A 903 1555 1555 2.40 LINK ZN ZN A 901 OXT BAL A 902 1555 1555 1.84 LINK NA NA A 903 O HOH A1173 1555 1555 2.48 LINK NA NA A 903 O HOH A1229 1555 1555 2.34 LINK NA NA A 904 O HOH A1187 1555 1555 2.39 CISPEP 1 GLU A 121 ALA A 122 0 4.90 CISPEP 2 ALA A 707 ASN A 708 0 1.12 SITE 1 AC1 4 HIS A 297 HIS A 301 GLU A 320 BAL A 902 SITE 1 AC2 11 GLU A 121 ALA A 262 MET A 263 GLU A 264 SITE 2 AC2 11 HIS A 297 GLU A 298 HIS A 301 LYS A 319 SITE 3 AC2 11 GLU A 320 TYR A 381 ZN A 901 SITE 1 AC3 5 SER A 332 ASP A 333 GLY A 335 HOH A1173 SITE 2 AC3 5 HOH A1229 SITE 1 AC4 4 GLN A 19 ILE A 20 LEU A 138 HOH A1187 SITE 1 AC5 6 LEU A 532 LEU A 554 ASP A 566 ALA A 567 SITE 2 AC5 6 SER A 570 HOH A1030 SITE 1 AC6 4 ARG A 161 ARG A 198 GLU A 212 TYR A 214 CRYST1 120.884 120.884 170.379 90.00 90.00 120.00 P 31 2 1 6 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 0.008272 0.004776 0.000000 0.00000 SCALE2 0.000000 0.009552 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005869 0.00000