HEADER PEPTIDE TRANSPORT 25-JUL-95 1DPE TITLE DIPEPTIDE-BINDING PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIPEPTIDE-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DIPEPTIDE PERMEASE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12 KEYWDS PEPTIDE TRANSPORT, PERIPLASMIC, CHEMOTAXIS BINDING PROTEINS FOR KEYWDS 2 ACTIVE TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR A.V.NICKITENKO,S.TRAKHANOV,F.A.QUIOCHO REVDAT 3 21-MAR-18 1DPE 1 REMARK REVDAT 2 24-FEB-09 1DPE 1 VERSN REVDAT 1 17-AUG-96 1DPE 0 JRNL AUTH A.V.NICKITENKO,S.TRAKHANOV,F.A.QUIOCHO JRNL TITL 2 A RESOLUTION STRUCTURE OF DPPA, A PERIPLASMIC DIPEPTIDE JRNL TITL 2 TRANSPORT/CHEMOSENSORY RECEPTOR. JRNL REF BIOCHEMISTRY V. 34 16585 1995 JRNL REFN ISSN 0006-2960 JRNL PMID 8527431 JRNL DOI 10.1021/BI00051A006 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 3 NUMBER OF REFLECTIONS : 36597 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL 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) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4046 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 488 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.014 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.038 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.044 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.022 ; 0.030 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.035 ; 0.060 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.188 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.265 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : 0.226 ; 0.300 REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 4.156 ; 15.000 REMARK 3 STAGGERED (DEGREES) : 16.470; 20.000 REMARK 3 TRANSVERSE (DEGREES) : 29.920; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.200 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.809 ; 2.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.885 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.815 ; 2.500 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DPE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000172885. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.073 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : FUJI REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 3.860 REMARK 200 R MERGE (I) : 0.06500 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 59.13500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.48500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.89000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.48500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 59.13500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.89000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 329 CG CD OE1 OE2 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 NE2 GLN A 188 O HOH A 788 2.11 REMARK 500 O HOH A 721 O HOH A 955 2.15 REMARK 500 O HOH A 742 O HOH A 743 2.16 REMARK 500 O HOH A 608 O HOH A 609 2.18 REMARK 500 OE2 GLU A 113 O HOH A 723 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 ARG A 68 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ASP A 88 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP A 95 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 132 CB - CG - OD1 ANGL. DEV. = 8.7 DEGREES REMARK 500 ARG A 141 NE - CZ - NH1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG A 195 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 TYR A 239 CB - CG - CD2 ANGL. DEV. = 4.7 DEGREES REMARK 500 TYR A 239 CB - CG - CD1 ANGL. DEV. = -4.9 DEGREES REMARK 500 ASP A 244 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG A 282 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 ASP A 319 CB - CG - OD1 ANGL. DEV. = 10.4 DEGREES REMARK 500 ASP A 320 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A 347 CB - CG - OD1 ANGL. DEV. = 7.6 DEGREES REMARK 500 ASP A 347 CB - CG - OD2 ANGL. DEV. = -7.0 DEGREES REMARK 500 ARG A 362 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ASP A 371 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 GLU A 385 OE1 - CD - OE2 ANGL. DEV. = -11.7 DEGREES REMARK 500 ARG A 392 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 GLU A 397 OE1 - CD - OE2 ANGL. DEV. = -7.5 DEGREES REMARK 500 GLU A 419 OE1 - CD - OE2 ANGL. DEV. = -9.7 DEGREES REMARK 500 CYS A 435 CB - CA - C ANGL. DEV. = 7.3 DEGREES REMARK 500 ASP A 451 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ASP A 451 CB - CG - OD2 ANGL. DEV. = -8.4 DEGREES REMARK 500 ASP A 468 CB - CG - OD1 ANGL. DEV. = 6.5 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 SER A 28 -83.32 -121.81 REMARK 500 TYR A 112 59.77 -99.03 REMARK 500 THR A 171 55.11 -142.38 REMARK 500 SER A 194 -70.51 -135.84 REMARK 500 TYR A 239 70.43 34.45 REMARK 500 ASP A 327 85.35 -151.35 REMARK 500 ASN A 358 89.18 -169.09 REMARK 500 ASN A 360 78.10 -150.65 REMARK 500 ALA A 470 62.17 31.35 REMARK 500 ILE A 475 -62.48 -99.24 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 CD A 508 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 66 NE2 REMARK 620 2 HOH A 698 O 93.8 REMARK 620 3 HOH A 697 O 162.6 97.3 REMARK 620 4 GLU A 55 OE2 87.8 139.0 75.0 REMARK 620 5 GLU A 55 OE1 99.7 89.5 67.1 50.1 REMARK 620 6 ASP A 395 OD1 87.7 136.6 93.3 84.4 133.1 REMARK 620 7 ASP A 395 OD2 97.2 87.7 96.6 132.7 163.0 49.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 509 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 699 O REMARK 620 2 HOH A 984 O 84.9 REMARK 620 3 GLU A 457 OE2 75.2 93.3 REMARK 620 4 GLU A 457 OE1 124.3 85.8 50.7 REMARK 620 5 HIS A 105 NE2 94.7 179.1 87.4 95.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 510 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 690 O REMARK 620 2 HOH A 691 O 171.1 REMARK 620 3 HOH A 692 O 92.0 79.2 REMARK 620 4 HOH A 693 O 94.5 94.4 170.6 REMARK 620 5 HOH A 694 O 91.2 90.8 92.5 80.5 REMARK 620 6 HIS A 467 NE2 97.4 81.8 94.0 91.9 169.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 511 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 667 O REMARK 620 2 GLU A 45 OE1 135.4 REMARK 620 3 GLU A 45 OE2 91.0 52.5 REMARK 620 4 HIS A 452 NE2 109.6 81.7 126.9 REMARK 620 5 GLU A 122 OE2 110.9 90.3 81.7 129.0 REMARK 620 6 GLU A 122 OE1 94.2 128.2 131.2 96.6 51.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 512 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 116 OE1 REMARK 620 2 HOH A 707 O 102.7 REMARK 620 3 HOH A 708 O 92.2 160.1 REMARK 620 4 ASP A 451 OD2 148.2 59.4 101.2 REMARK 620 5 ASP A 451 OD1 109.2 74.3 88.5 43.5 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 CD A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 512 DBREF 1DPE A 1 507 UNP P23847 DPPA_ECOLI 29 535 SEQADV 1DPE ILE A 20 UNP P23847 THR 48 CONFLICT SEQADV 1DPE GLU A 419 UNP P23847 LEU 447 CONFLICT SEQRES 1 A 507 LYS THR LEU VAL TYR CYS SER GLU GLY SER PRO GLU GLY SEQRES 2 A 507 PHE ASN PRO GLN LEU PHE ILE SER GLY THR THR TYR ASP SEQRES 3 A 507 ALA SER SER VAL PRO LEU TYR ASN ARG LEU VAL GLU PHE SEQRES 4 A 507 LYS ILE GLY THR THR GLU VAL ILE PRO GLY LEU ALA GLU SEQRES 5 A 507 LYS TRP GLU VAL SER GLU ASP GLY LYS THR TYR THR PHE SEQRES 6 A 507 HIS LEU ARG LYS GLY VAL LYS TRP HIS ASP ASN LYS GLU SEQRES 7 A 507 PHE LYS PRO THR ARG GLU LEU ASN ALA ASP ASP VAL VAL SEQRES 8 A 507 PHE SER PHE ASP ARG GLN LYS ASN ALA GLN ASN PRO TYR SEQRES 9 A 507 HIS LYS VAL SER GLY GLY SER TYR GLU TYR PHE GLU GLY SEQRES 10 A 507 MET GLY LEU PRO GLU LEU ILE SER GLU VAL LYS LYS VAL SEQRES 11 A 507 ASP ASP ASN THR VAL GLN PHE VAL LEU THR ARG PRO GLU SEQRES 12 A 507 ALA PRO PHE LEU ALA ASP LEU ALA MET ASP PHE ALA SER SEQRES 13 A 507 ILE LEU SER LYS GLU TYR ALA ASP ALA MET MET LYS ALA SEQRES 14 A 507 GLY THR PRO GLU LYS LEU ASP LEU ASN PRO ILE GLY THR SEQRES 15 A 507 GLY PRO PHE GLN LEU GLN GLN TYR GLN LYS ASP SER ARG SEQRES 16 A 507 ILE ARG TYR LYS ALA PHE ASP GLY TYR TRP GLY THR LYS SEQRES 17 A 507 PRO GLN ILE ASP THR LEU VAL PHE SER ILE THR PRO ASP SEQRES 18 A 507 ALA SER VAL ARG TYR ALA LYS LEU GLN LYS ASN GLU CYS SEQRES 19 A 507 GLN VAL MET PRO TYR PRO ASN PRO ALA ASP ILE ALA ARG SEQRES 20 A 507 MET LYS GLN ASP LYS SER ILE ASN LEU MET GLU MET PRO SEQRES 21 A 507 GLY LEU ASN VAL GLY TYR LEU SER TYR ASN VAL GLN LYS SEQRES 22 A 507 LYS PRO LEU ASP ASP VAL LYS VAL ARG GLN ALA LEU THR SEQRES 23 A 507 TYR ALA VAL ASN LYS ASP ALA ILE ILE LYS ALA VAL TYR SEQRES 24 A 507 GLN GLY ALA GLY VAL SER ALA LYS ASN LEU ILE PRO PRO SEQRES 25 A 507 THR MET TRP GLY TYR ASN ASP ASP VAL GLN ASP TYR THR SEQRES 26 A 507 TYR ASP PRO GLU LYS ALA LYS ALA LEU LEU LYS GLU ALA SEQRES 27 A 507 GLY LEU GLU LYS GLY PHE SER ILE ASP LEU TRP ALA MET SEQRES 28 A 507 PRO VAL GLN ARG PRO TYR ASN PRO ASN ALA ARG ARG MET SEQRES 29 A 507 ALA GLU MET ILE GLN ALA ASP TRP ALA LYS VAL GLY VAL SEQRES 30 A 507 GLN ALA LYS ILE VAL THR TYR GLU TRP GLY GLU TYR LEU SEQRES 31 A 507 LYS ARG ALA LYS ASP GLY GLU HIS GLN THR VAL MET MET SEQRES 32 A 507 GLY TRP THR GLY ASP ASN GLY ASP PRO ASP ASN PHE PHE SEQRES 33 A 507 ALA THR GLU PHE SER CYS ALA ALA SER GLU GLN GLY SER SEQRES 34 A 507 ASN TYR SER LYS TRP CYS TYR LYS PRO PHE GLU ASP LEU SEQRES 35 A 507 ILE GLN PRO ALA ARG ALA THR ASP ASP HIS ASN LYS ARG SEQRES 36 A 507 VAL GLU LEU TYR LYS GLN ALA GLN VAL VAL MET HIS ASP SEQRES 37 A 507 GLN ALA PRO ALA LEU ILE ILE ALA HIS SER THR VAL PHE SEQRES 38 A 507 GLU PRO VAL ARG LYS GLU VAL LYS GLY TYR VAL VAL ASP SEQRES 39 A 507 PRO LEU GLY LYS HIS HIS PHE GLU ASN VAL SER ILE GLU HET CD A 508 1 HET CD A 509 1 HET CD A 510 1 HET CD A 511 1 HET CD A 512 1 HETNAM CD CADMIUM ION FORMUL 2 CD 5(CD 2+) FORMUL 7 HOH *488(H2 O) HELIX 1 1 GLY A 22 ALA A 27 1 6 HELIX 2 2 ALA A 87 LYS A 98 1 12 HELIX 3 3 GLU A 113 GLY A 117 1 5 HELIX 4 4 ALA A 144 ALA A 151 5 8 HELIX 5 5 LYS A 160 LYS A 168 1 9 HELIX 6 6 PRO A 172 LEU A 177 5 6 HELIX 7 7 ALA A 222 GLN A 230 1 9 HELIX 8 8 PRO A 242 GLN A 250 5 9 HELIX 9 9 VAL A 279 TYR A 287 1 9 HELIX 10 10 LYS A 291 TYR A 299 1 9 HELIX 11 11 PRO A 328 GLU A 337 1 10 HELIX 12 12 ALA A 361 VAL A 375 1 15 HELIX 13 13 TRP A 386 ASP A 395 1 10 HELIX 14 14 PRO A 412 PHE A 420 5 9 HELIX 15 15 CYS A 422 GLN A 427 1 6 HELIX 16 16 LYS A 437 ALA A 448 1 12 HELIX 17 17 HIS A 452 GLN A 469 1 18 SHEET 1 A 7 ILE A 254 PRO A 260 0 SHEET 2 A 7 THR A 479 ARG A 485 -1 N VAL A 484 O ASN A 255 SHEET 3 A 7 VAL A 236 MET A 237 -1 N MET A 237 O PRO A 483 SHEET 4 A 7 THR A 2 SER A 7 1 N CYS A 6 O VAL A 236 SHEET 5 A 7 THR A 213 ILE A 218 1 N THR A 213 O LEU A 3 SHEET 6 A 7 ARG A 195 ALA A 200 -1 N TYR A 198 O LEU A 214 SHEET 7 A 7 PHE A 185 GLN A 191 -1 N GLN A 191 O ARG A 195 SHEET 1 B 2 VAL A 37 PHE A 39 0 SHEET 2 B 2 VAL A 46 PRO A 48 -1 N ILE A 47 O GLU A 38 SHEET 1 C 4 ALA A 51 VAL A 56 0 SHEET 2 C 4 THR A 62 LEU A 67 -1 N HIS A 66 O GLU A 52 SHEET 3 C 4 THR A 134 LEU A 139 -1 N PHE A 137 O TYR A 63 SHEET 4 C 4 ILE A 124 LYS A 129 -1 N LYS A 128 O GLN A 136 SHEET 1 D 6 VAL A 377 VAL A 382 0 SHEET 2 D 6 PHE A 344 TRP A 349 1 N ILE A 346 O GLN A 378 SHEET 3 D 6 THR A 400 THR A 406 1 N THR A 400 O TRP A 349 SHEET 4 D 6 ASN A 263 TYR A 269 -1 N SER A 268 O VAL A 401 SHEET 5 D 6 ALA A 472 SER A 478 -1 N ALA A 476 O GLY A 265 SHEET 6 D 6 GLY A 303 SER A 305 -1 N VAL A 304 O HIS A 477 SHEET 1 E 2 VAL A 488 LYS A 489 0 SHEET 2 E 2 SER A 505 ILE A 506 -1 N SER A 505 O LYS A 489 SSBOND 1 CYS A 6 CYS A 234 1555 1555 2.20 SSBOND 2 CYS A 422 CYS A 435 1555 1555 2.03 LINK CD CD A 508 NE2 HIS A 66 1555 1555 2.31 LINK CD CD A 508 O HOH A 698 1555 1555 2.45 LINK CD CD A 508 O HOH A 697 1555 1555 1.65 LINK CD CD A 508 OE2 GLU A 55 1555 1555 2.55 LINK CD CD A 508 OE1 GLU A 55 1555 1555 2.49 LINK CD CD A 509 O HOH A 699 1555 1555 2.58 LINK CD CD A 509 O HOH A 984 1555 1555 2.52 LINK CD CD A 509 OE2 GLU A 457 1555 1555 2.62 LINK CD CD A 509 OE1 GLU A 457 1555 1555 2.48 LINK CD CD A 510 O HOH A 690 1555 1555 2.53 LINK CD CD A 510 O HOH A 691 1555 1555 2.48 LINK CD CD A 510 O HOH A 692 1555 1555 2.26 LINK CD CD A 510 O HOH A 693 1555 1555 2.40 LINK CD CD A 510 O HOH A 694 1555 1555 2.85 LINK CD CD A 510 NE2 HIS A 467 1555 1555 2.48 LINK CD CD A 511 O HOH A 667 1555 1555 2.12 LINK CD CD A 511 OE1 GLU A 45 1555 1555 2.62 LINK CD CD A 511 OE2 GLU A 45 1555 1555 2.21 LINK CD CD A 511 NE2 HIS A 452 1555 1555 2.32 LINK CD CD A 512 OE1 GLU A 116 1555 1555 2.70 LINK CD CD A 512 O HOH A 707 1555 1555 1.87 LINK CD CD A 512 O HOH A 708 1555 1555 2.55 LINK CD CD A 508 OD1 ASP A 395 1555 2564 2.79 LINK CD CD A 508 OD2 ASP A 395 1555 2564 2.43 LINK CD CD A 509 NE2 HIS A 105 1555 2564 2.34 LINK CD CD A 511 OE2 GLU A 122 1555 2564 2.53 LINK CD CD A 511 OE1 GLU A 122 1555 2564 2.56 LINK CD CD A 512 OD2 ASP A 451 1555 2565 2.89 LINK CD CD A 512 OD1 ASP A 451 1555 2565 3.14 CISPEP 1 LYS A 274 PRO A 275 0 0.26 SITE 1 AC1 5 GLU A 55 HIS A 66 ASP A 395 HOH A 697 SITE 2 AC1 5 HOH A 698 SITE 1 AC2 4 HIS A 105 GLU A 457 HOH A 699 HOH A 984 SITE 1 AC3 6 HIS A 467 HOH A 690 HOH A 691 HOH A 692 SITE 2 AC3 6 HOH A 693 HOH A 694 SITE 1 AC4 4 GLU A 45 GLU A 122 HIS A 452 HOH A 667 SITE 1 AC5 4 GLU A 116 ASP A 451 HOH A 707 HOH A 708 CRYST1 118.270 79.780 62.970 90.00 90.00 90.00 P 21 21 21 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 0.008455 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012534 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015881 0.00000