HEADER METAL BINDING PROTEIN 25-JUL-16 5KZJ TITLE LOOP DELETION MUTANT OF PARACOCCUS DENITRIFICANS AZTC COMPND MOL_ID: 1; COMPND 2 MOLECULE: PERIPLASMIC SOLUTE BINDING PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PARACOCCUS DENITRIFICANS (STRAIN PD 1222); SOURCE 3 ORGANISM_TAXID: 318586; SOURCE 4 STRAIN: PD 1222; SOURCE 5 GENE: PDEN_1597; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET45 KEYWDS ZINC BINDING PROTEIN, PERIPLASM, DELETION MUTANT, METAL BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.YUKL REVDAT 6 23-OCT-24 5KZJ 1 REMARK REVDAT 5 04-OCT-23 5KZJ 1 REMARK REVDAT 4 25-DEC-19 5KZJ 1 REMARK REVDAT 3 01-NOV-17 5KZJ 1 JRNL REVDAT 2 20-SEP-17 5KZJ 1 JRNL REVDAT 1 05-JUL-17 5KZJ 0 JRNL AUTH D.P.NEUPANE,D.AVALOS,S.FULLAM,H.ROYCHOWDHURY,E.T.YUKL JRNL TITL MECHANISMS OF ZINC BINDING TO THE SOLUTE-BINDING PROTEIN JRNL TITL 2 AZTC AND TRANSFER FROM THE METALLOCHAPERONE AZTD. JRNL REF J. BIOL. CHEM. V. 292 17496 2017 JRNL REFN ESSN 1083-351X JRNL PMID 28887302 JRNL DOI 10.1074/JBC.M117.804799 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 36792 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) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1945 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.25 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2592 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.08 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE SET COUNT : 133 REMARK 3 BIN FREE R VALUE : 0.2590 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3963 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 162 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.19 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.87000 REMARK 3 B22 (A**2) : 4.85000 REMARK 3 B33 (A**2) : -2.30000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.07000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.163 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.151 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.116 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.134 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4108 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3851 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5615 ; 1.910 ; 1.950 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8797 ; 0.943 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 553 ; 7.603 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 187 ;37.533 ;24.064 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 571 ;16.606 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;20.942 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 643 ; 0.124 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4899 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 938 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 25 A 309 REMARK 3 ORIGIN FOR THE GROUP (A): -14.5612 -38.9460 -18.7176 REMARK 3 T TENSOR REMARK 3 T11: 0.0756 T22: 0.0312 REMARK 3 T33: 0.1281 T12: 0.0153 REMARK 3 T13: 0.0038 T23: -0.0248 REMARK 3 L TENSOR REMARK 3 L11: 0.9237 L22: 0.8222 REMARK 3 L33: 0.2168 L12: -0.6242 REMARK 3 L13: -0.3260 L23: 0.3742 REMARK 3 S TENSOR REMARK 3 S11: -0.0563 S12: 0.0246 S13: -0.0078 REMARK 3 S21: 0.0897 S22: -0.0184 S23: 0.1194 REMARK 3 S31: 0.0569 S32: 0.0126 S33: 0.0747 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 25 B 308 REMARK 3 ORIGIN FOR THE GROUP (A): -2.2259 -1.0916 -13.6879 REMARK 3 T TENSOR REMARK 3 T11: 0.1159 T22: 0.0350 REMARK 3 T33: 0.1007 T12: -0.0242 REMARK 3 T13: -0.0135 T23: 0.0004 REMARK 3 L TENSOR REMARK 3 L11: 0.6233 L22: 0.6105 REMARK 3 L33: 0.4364 L12: 0.4676 REMARK 3 L13: -0.3579 L23: -0.3123 REMARK 3 S TENSOR REMARK 3 S11: 0.0959 S12: -0.0989 S13: 0.0881 REMARK 3 S21: 0.0080 S22: -0.1210 S23: 0.1111 REMARK 3 S31: 0.0335 S32: 0.0763 S33: 0.0252 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 5KZJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1000222727. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAY-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.09998 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38783 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.6180 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.46100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.312 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4XRV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4.0 - 5.0 M SODIUM FORMATE, 0.1 M BIS REMARK 280 -TRIS PROPANE, PH 7.0, BATCH MODE, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 52.15700 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 MET A 1 REMARK 465 LYS A 2 REMARK 465 ASP A 3 REMARK 465 TRP A 4 REMARK 465 LEU A 5 REMARK 465 PHE A 6 REMARK 465 ARG A 7 REMARK 465 ILE A 8 REMARK 465 ALA A 9 REMARK 465 THR A 10 REMARK 465 CYS A 11 REMARK 465 SER A 12 REMARK 465 ILE A 13 REMARK 465 MET A 14 REMARK 465 THR A 15 REMARK 465 PHE A 16 REMARK 465 SER A 17 REMARK 465 SER A 18 REMARK 465 LEU A 19 REMARK 465 ALA A 20 REMARK 465 ALA A 21 REMARK 465 ALA A 22 REMARK 465 GLN A 23 REMARK 465 ALA A 24 REMARK 465 MET B 1 REMARK 465 LYS B 2 REMARK 465 ASP B 3 REMARK 465 TRP B 4 REMARK 465 LEU B 5 REMARK 465 PHE B 6 REMARK 465 ARG B 7 REMARK 465 ILE B 8 REMARK 465 ALA B 9 REMARK 465 THR B 10 REMARK 465 CYS B 11 REMARK 465 SER B 12 REMARK 465 ILE B 13 REMARK 465 MET B 14 REMARK 465 THR B 15 REMARK 465 PHE B 16 REMARK 465 SER B 17 REMARK 465 SER B 18 REMARK 465 LEU B 19 REMARK 465 ALA B 20 REMARK 465 ALA B 21 REMARK 465 ALA B 22 REMARK 465 GLN B 23 REMARK 465 ALA B 24 REMARK 465 ARG B 309 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 GLU A 185 NH2 ARG A 296 2.14 REMARK 500 O3 GOL A 403 O HOH A 501 2.16 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 136 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ARG A 208 NE - CZ - NH1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG A 208 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG B 92 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG B 92 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG B 208 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG B 296 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG B 296 NE - CZ - NH2 ANGL. DEV. = -5.2 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 HIS A 138 44.66 -80.48 REMARK 500 ASP A 161 80.68 -151.54 REMARK 500 PRO A 194 132.65 -37.44 REMARK 500 SER A 228 -131.10 -72.11 REMARK 500 GLU A 229 -86.15 -129.00 REMARK 500 ALA A 230 -54.72 165.51 REMARK 500 ALA A 231 60.65 36.60 REMARK 500 SER A 278 -72.55 -93.88 REMARK 500 ASP A 285 -5.74 72.14 REMARK 500 PRO B 65 95.34 -34.82 REMARK 500 PRO B 67 -56.22 -8.28 REMARK 500 HIS B 138 43.48 -77.22 REMARK 500 ASP B 161 74.02 -152.21 REMARK 500 ARG B 197 77.14 -119.58 REMARK 500 ALA B 247 123.62 -33.27 REMARK 500 GLU B 267 3.65 -43.33 REMARK 500 ALA B 268 11.92 -149.37 REMARK 500 SER B 278 -76.33 -93.15 REMARK 500 ALA B 288 51.71 -144.13 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 228 GLU A 229 -149.17 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 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 61 NE2 REMARK 620 2 HIS A 138 NE2 113.9 REMARK 620 3 HIS A 204 NE2 112.7 120.5 REMARK 620 4 ASP A 279 OD2 94.1 109.5 101.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 61 NE2 REMARK 620 2 HIS B 138 NE2 111.7 REMARK 620 3 HIS B 204 NE2 110.4 113.5 REMARK 620 4 ASP B 279 OD2 96.0 115.0 108.8 REMARK 620 N 1 2 3 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 GOL A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4XRV RELATED DB: PDB REMARK 900 THE CURRENT STRUCTURE IS A DELETION MUTANT OF 4XRV LACKING RESIDUES REMARK 900 120-132. DBREF 5KZJ A 1 309 UNP A1B2F3 A1B2F3_PARDP 1 309 DBREF 5KZJ B 1 309 UNP A1B2F3 A1B2F3_PARDP 1 309 SEQADV 5KZJ A UNP A1B2F3 HIS 120 DELETION SEQADV 5KZJ A UNP A1B2F3 TYR 121 DELETION SEQADV 5KZJ A UNP A1B2F3 HIS 122 DELETION SEQADV 5KZJ A UNP A1B2F3 TYR 123 DELETION SEQADV 5KZJ A UNP A1B2F3 ILE 124 DELETION SEQADV 5KZJ A UNP A1B2F3 ASP 125 DELETION SEQADV 5KZJ A UNP A1B2F3 GLY 126 DELETION SEQADV 5KZJ A UNP A1B2F3 LYS 127 DELETION SEQADV 5KZJ A UNP A1B2F3 ALA 128 DELETION SEQADV 5KZJ A UNP A1B2F3 VAL 129 DELETION SEQADV 5KZJ A UNP A1B2F3 PHE 130 DELETION SEQADV 5KZJ A UNP A1B2F3 HIS 131 DELETION SEQADV 5KZJ A UNP A1B2F3 ALA 132 DELETION SEQADV 5KZJ B UNP A1B2F3 HIS 120 DELETION SEQADV 5KZJ B UNP A1B2F3 TYR 121 DELETION SEQADV 5KZJ B UNP A1B2F3 HIS 122 DELETION SEQADV 5KZJ B UNP A1B2F3 TYR 123 DELETION SEQADV 5KZJ B UNP A1B2F3 ILE 124 DELETION SEQADV 5KZJ B UNP A1B2F3 ASP 125 DELETION SEQADV 5KZJ B UNP A1B2F3 GLY 126 DELETION SEQADV 5KZJ B UNP A1B2F3 LYS 127 DELETION SEQADV 5KZJ B UNP A1B2F3 ALA 128 DELETION SEQADV 5KZJ B UNP A1B2F3 VAL 129 DELETION SEQADV 5KZJ B UNP A1B2F3 PHE 130 DELETION SEQADV 5KZJ B UNP A1B2F3 HIS 131 DELETION SEQADV 5KZJ B UNP A1B2F3 ALA 132 DELETION SEQRES 1 A 296 MET LYS ASP TRP LEU PHE ARG ILE ALA THR CYS SER ILE SEQRES 2 A 296 MET THR PHE SER SER LEU ALA ALA ALA GLN ALA GLU PRO SEQRES 3 A 296 LEU ASP VAL VAL ALA THR PHE SER ILE ILE GLY ASP PHE SEQRES 4 A 296 ALA ALA LYS VAL GLY GLY ASP ARG ILE ARG LEU ASN VAL SEQRES 5 A 296 LEU VAL GLY PRO ASP SER ASP THR HIS VAL TYR GLU PRO SEQRES 6 A 296 ARG PRO ALA ASP ALA ILE ALA LEU ALA GLY ALA ASP VAL SEQRES 7 A 296 VAL LEU THR ASN GLY LEU GLU PHE GLU GLY PHE LEU THR SEQRES 8 A 296 ARG LEU ILE ALA ALA SER GLY THR ASP ALA ALA VAL ALA SEQRES 9 A 296 THR LEU THR ASP GLY VAL GLU THR MET GLU GLU PRO GLY SEQRES 10 A 296 GLY GLY GLY ALA HIS ASP PRO HIS ALA TRP GLN ALA VAL SEQRES 11 A 296 PRO ASN ALA LYS VAL TYR VAL GLN ASN ILE ALA ALA ALA SEQRES 12 A 296 PHE CYS ALA ALA ASP ALA GLU GLY CYS ALA ALA TYR GLN SEQRES 13 A 296 ALA ASN ALA ALA ARG TYR ILE GLY GLU LEU ASP ALA LEU SEQRES 14 A 296 ASP THR GLU ILE ARG ALA ALA ILE ALA ALA LEU PRO GLN SEQRES 15 A 296 ASP ARG ARG THR VAL VAL VAL ALA HIS ASN ALA PHE ARG SEQRES 16 A 296 TYR PHE GLU ALA ALA TYR GLY VAL HIS PHE LEU SER PRO SEQRES 17 A 296 GLN GLY VAL SER THR GLU SER GLU ALA ALA ALA ALA ASP SEQRES 18 A 296 VAL ALA GLY LEU ILE ARG GLU ILE ARG ALA ARG ASN ALA SEQRES 19 A 296 SER ALA ILE PHE ALA GLU ASN ILE SER ASP THR ARG LEU SEQRES 20 A 296 LEU GLU GLN ILE ALA ARG GLU ALA GLY LEU PRO LEU ALA SEQRES 21 A 296 GLY THR LEU TYR SER ASP ALA LEU SER GLY PRO ASP GLY SEQRES 22 A 296 PRO ALA SER ASN TYR ILE ALA MET MET ARG HIS ASN ALA SEQRES 23 A 296 GLY ALA ILE ALA ALA ALA LEU ALA ALA ARG SEQRES 1 B 296 MET LYS ASP TRP LEU PHE ARG ILE ALA THR CYS SER ILE SEQRES 2 B 296 MET THR PHE SER SER LEU ALA ALA ALA GLN ALA GLU PRO SEQRES 3 B 296 LEU ASP VAL VAL ALA THR PHE SER ILE ILE GLY ASP PHE SEQRES 4 B 296 ALA ALA LYS VAL GLY GLY ASP ARG ILE ARG LEU ASN VAL SEQRES 5 B 296 LEU VAL GLY PRO ASP SER ASP THR HIS VAL TYR GLU PRO SEQRES 6 B 296 ARG PRO ALA ASP ALA ILE ALA LEU ALA GLY ALA ASP VAL SEQRES 7 B 296 VAL LEU THR ASN GLY LEU GLU PHE GLU GLY PHE LEU THR SEQRES 8 B 296 ARG LEU ILE ALA ALA SER GLY THR ASP ALA ALA VAL ALA SEQRES 9 B 296 THR LEU THR ASP GLY VAL GLU THR MET GLU GLU PRO GLY SEQRES 10 B 296 GLY GLY GLY ALA HIS ASP PRO HIS ALA TRP GLN ALA VAL SEQRES 11 B 296 PRO ASN ALA LYS VAL TYR VAL GLN ASN ILE ALA ALA ALA SEQRES 12 B 296 PHE CYS ALA ALA ASP ALA GLU GLY CYS ALA ALA TYR GLN SEQRES 13 B 296 ALA ASN ALA ALA ARG TYR ILE GLY GLU LEU ASP ALA LEU SEQRES 14 B 296 ASP THR GLU ILE ARG ALA ALA ILE ALA ALA LEU PRO GLN SEQRES 15 B 296 ASP ARG ARG THR VAL VAL VAL ALA HIS ASN ALA PHE ARG SEQRES 16 B 296 TYR PHE GLU ALA ALA TYR GLY VAL HIS PHE LEU SER PRO SEQRES 17 B 296 GLN GLY VAL SER THR GLU SER GLU ALA ALA ALA ALA ASP SEQRES 18 B 296 VAL ALA GLY LEU ILE ARG GLU ILE ARG ALA ARG ASN ALA SEQRES 19 B 296 SER ALA ILE PHE ALA GLU ASN ILE SER ASP THR ARG LEU SEQRES 20 B 296 LEU GLU GLN ILE ALA ARG GLU ALA GLY LEU PRO LEU ALA SEQRES 21 B 296 GLY THR LEU TYR SER ASP ALA LEU SER GLY PRO ASP GLY SEQRES 22 B 296 PRO ALA SER ASN TYR ILE ALA MET MET ARG HIS ASN ALA SEQRES 23 B 296 GLY ALA ILE ALA ALA ALA LEU ALA ALA ARG HET ZN A 401 1 HET GOL A 402 6 HET GOL A 403 6 HET ZN B 401 1 HETNAM ZN ZINC ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ZN 2(ZN 2+) FORMUL 4 GOL 2(C3 H8 O3) FORMUL 7 HOH *162(H2 O) HELIX 1 AA1 SER A 34 GLY A 45 1 12 HELIX 2 AA2 ASP A 59 TYR A 63 5 5 HELIX 3 AA3 ARG A 66 GLY A 75 1 10 HELIX 4 AA4 PHE A 89 SER A 97 1 9 HELIX 5 AA5 HIS A 138 GLN A 141 5 4 HELIX 6 AA6 ALA A 142 ASP A 161 1 20 HELIX 7 AA7 GLY A 164 LEU A 193 1 30 HELIX 8 AA8 PHE A 207 GLY A 215 1 9 HELIX 9 AA9 ALA A 231 ALA A 233 5 3 HELIX 10 AB1 ASP A 234 ARG A 245 1 12 HELIX 11 AB2 THR A 258 GLY A 269 1 12 HELIX 12 AB3 ASN A 290 ARG A 309 1 20 HELIX 13 AB4 SER B 34 GLY B 45 1 12 HELIX 14 AB5 ASP B 59 TYR B 63 5 5 HELIX 15 AB6 ARG B 66 ALA B 76 1 11 HELIX 16 AB7 PHE B 89 GLY B 98 1 10 HELIX 17 AB8 HIS B 138 GLN B 141 5 4 HELIX 18 AB9 ALA B 142 ASP B 161 1 20 HELIX 19 AC1 GLY B 164 ALA B 192 1 29 HELIX 20 AC2 PHE B 207 GLY B 215 1 9 HELIX 21 AC3 ALA B 231 ASN B 246 1 16 HELIX 22 AC4 THR B 258 GLU B 267 1 10 HELIX 23 AC5 ASN B 290 ALA B 308 1 19 SHEET 1 AA1 4 ILE A 48 VAL A 54 0 SHEET 2 AA1 4 LEU A 27 PHE A 33 1 N LEU A 27 O ARG A 49 SHEET 3 AA1 4 VAL A 78 THR A 81 1 O LEU A 80 N VAL A 30 SHEET 4 AA1 4 ALA A 102 THR A 105 1 O ALA A 102 N VAL A 79 SHEET 1 AA2 2 MET A 113 GLU A 114 0 SHEET 2 AA2 2 HIS A 135 ASP A 136 -1 O ASP A 136 N MET A 113 SHEET 1 AA3 4 HIS A 217 LEU A 219 0 SHEET 2 AA3 4 THR A 199 VAL A 201 1 N VAL A 200 O LEU A 219 SHEET 3 AA3 4 ALA A 249 GLU A 253 1 O ALA A 249 N VAL A 201 SHEET 4 AA3 4 LEU A 272 LEU A 276 1 O LEU A 276 N ALA A 252 SHEET 1 AA4 4 ILE B 48 VAL B 54 0 SHEET 2 AA4 4 LEU B 27 PHE B 33 1 N THR B 32 O VAL B 54 SHEET 3 AA4 4 VAL B 78 THR B 81 1 O LEU B 80 N VAL B 30 SHEET 4 AA4 4 ALA B 102 THR B 105 1 O ALA B 104 N VAL B 79 SHEET 1 AA5 4 HIS B 217 LEU B 219 0 SHEET 2 AA5 4 THR B 199 VAL B 201 1 N VAL B 200 O HIS B 217 SHEET 3 AA5 4 ALA B 249 GLU B 253 1 O PHE B 251 N VAL B 201 SHEET 4 AA5 4 LEU B 272 LEU B 276 1 O LEU B 276 N ALA B 252 SSBOND 1 CYS A 158 CYS A 165 1555 1555 2.11 SSBOND 2 CYS B 158 CYS B 165 1555 1555 2.10 LINK NE2 HIS A 61 ZN ZN A 401 1555 1555 2.04 LINK NE2 HIS A 138 ZN ZN A 401 1555 1555 1.96 LINK NE2 HIS A 204 ZN ZN A 401 1555 1555 2.04 LINK OD2 ASP A 279 ZN ZN A 401 1555 1555 2.19 LINK NE2 HIS B 61 ZN ZN B 401 1555 1555 1.97 LINK NE2 HIS B 138 ZN ZN B 401 1555 1555 2.10 LINK NE2 HIS B 204 ZN ZN B 401 1555 1555 2.04 LINK OD2 ASP B 279 ZN ZN B 401 1555 1555 2.00 CISPEP 1 GLY A 118 GLY A 119 0 3.99 SITE 1 AC1 5 HIS A 61 HIS A 138 HIS A 204 VAL A 224 SITE 2 AC1 5 ASP A 279 SITE 1 AC2 7 PRO A 65 ARG A 66 PRO A 67 ARG A 92 SITE 2 AC2 7 ALA A 96 HOH A 504 HOH A 509 SITE 1 AC3 5 ARG A 296 HIS A 297 GLY A 300 HOH A 501 SITE 2 AC3 5 HOH A 547 SITE 1 AC4 5 HIS B 61 HIS B 138 HIS B 204 VAL B 224 SITE 2 AC4 5 ASP B 279 CRYST1 61.826 104.314 64.320 90.00 110.70 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016174 0.000000 0.006112 0.00000 SCALE2 0.000000 0.009586 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016620 0.00000