Header list of 1vl3.pdb file
Complete list - 25 201 Bytes
HEADER DE NOVO PROTEIN 05-JUL-04 1VL3
TITLE DESIGN OF NEW MIMOCHROMES WITH UNIQUE TOPOLOGY
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: GLU-SER-GLN-LEU-HIS-SER-ASN-LYS-ARG;
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED.
KEYWDS ALPHA-HELIX, DESIGN, MINIATURIZED METALLOPROTEINS, DE NOVO PROTEIN
EXPDTA SOLUTION NMR
AUTHOR A.LOMBARDI,F.NASTRI,D.MARASCO,O.MAGLIO,G.DE SANCTIS,F.SINIBALDI,
AUTHOR 2 R.SANTUCCI,M.COLETTA,V.PAVONE
REVDAT 3 31-AUG-11 1VL3 1 HETATM VERSN
REVDAT 2 24-FEB-09 1VL3 1 VERSN
REVDAT 1 20-JUL-04 1VL3 0
SPRSDE 20-JUL-04 1VL3 1L1B
JRNL AUTH A.LOMBARDI,F.NASTRI,D.MARASCO,O.MAGLIO,G.DE SANCTIS,
JRNL AUTH 2 F.SINIBALDI,R.SANTUCCI,M.COLETTA,V.PAVONE
JRNL TITL DESIGN OF A NEW MIMOCHROME WITH UNIQUE TOPOLOGY.
JRNL REF CHEMISTRY V. 9 5643 2003
JRNL REFN ISSN 0947-6539
JRNL PMID 14639648
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : DISCOVER
REMARK 3 AUTHORS : MSI
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON A TOTAL OF
REMARK 3 250 NOE-DERIVED DISTANCE RESTRAINTS
REMARK 4
REMARK 4 1VL3 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUL-04.
REMARK 100 THE RCSB ID CODE IS RCSB001969.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 5.5
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 1MM CO(III)-MIMOCHROME IV 70%
REMARK 210 H2O, 30% CF3CD2OD
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; TOCSY; DQF-COSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NMRPIPE, DISCOVER
REMARK 210 METHOD USED : MOLECULAR DYNAMIC SIMULATION FOR
REMARK 210 400 PS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D
REMARK 210 HOMONUCLEAR TECHNIQUES.
REMARK 215
REMARK 215 NMR STUDY
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
REMARK 215 THESE RECORDS ARE MEANINGLESS.
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: DIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
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 HH12 ARG A 9 OE2 GLU B 1 1.54
REMARK 500 HH22 ARG A 9 OE1 GLU B 1 1.55
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 ARG A 9 CZ ARG A 9 NH1 0.095
REMARK 500 ARG A 9 CZ ARG A 9 NH2 0.094
REMARK 500 ARG B 9 CZ ARG B 9 NH1 0.095
REMARK 500 ARG B 9 CZ ARG B 9 NH2 0.092
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 B 9 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES
REMARK 500 ARG B 9 NE - CZ - NH2 ANGL. DEV. = -5.4 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 2 -64.68 -25.72
REMARK 500 LYS A 8 -69.04 61.99
REMARK 500 SER B 2 -53.81 -25.46
REMARK 500 SER B 6 -23.92 -38.70
REMARK 500 LYS B 8 -48.90 13.05
REMARK 500
REMARK 500 REMARK: NULL
REMARK 610
REMARK 610 MISSING HETEROATOM
REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 610 I=INSERTION CODE):
REMARK 610 M RES C SSEQI
REMARK 610 DEU B 19
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 DEU B 19 CO
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 5 NE2
REMARK 620 2 DEU B 19 NA 93.0
REMARK 620 3 DEU B 19 NB 89.6 89.7
REMARK 620 4 DEU B 19 NC 89.2 177.7 89.8
REMARK 620 5 DEU B 19 ND 89.4 90.7 179.0 89.8
REMARK 620 6 HIS B 5 NE2 178.0 88.3 88.9 89.5 92.1
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 DEU B 19
DBREF 1VL3 A 0 10 PDB 1VL3 1VL3 0 10
DBREF 1VL3 B 0 10 PDB 1VL3 1VL3 0 10
SEQRES 1 A 11 ACE GLU SER GLN LEU HIS SER ASN LYS ARG NH2
SEQRES 1 B 11 ACE GLU SER GLN LEU HIS SER ASN LYS ARG NH2
HET ACE A 0 6
HET NH2 A 10 3
HET ACE B 0 6
HET NH2 B 10 3
HET DEU B 19 61
HETNAM ACE ACETYL GROUP
HETNAM NH2 AMINO GROUP
HETNAM DEU CO(III)-(DEUTEROPORPHYRIN IX)
FORMUL 1 ACE 2(C2 H4 O)
FORMUL 1 NH2 2(H2 N)
FORMUL 3 DEU C30 H28 CO N4 O4 5+
HELIX 1 1 GLU A 1 LYS A 8 1 8
HELIX 2 2 GLU B 1 SER B 6 1 6
LINK NZ LYS A 8 CGA DEU B 19 1555 1555 1.35
LINK NZ LYS B 8 CGD DEU B 19 1555 1555 1.33
LINK NE2 HIS A 5 CO DEU B 19 1555 1555 2.05
LINK NE2 HIS B 5 CO DEU B 19 1555 1555 2.04
LINK C ACE A 0 N GLU A 1 1555 1555 1.33
LINK C ARG A 9 N NH2 A 10 1555 1555 1.33
LINK C ACE B 0 N GLU B 1 1555 1555 1.32
LINK C ARG B 9 N NH2 B 10 1555 1555 1.33
SITE 1 AC1 8 GLU A 1 HIS A 5 ASN A 7 LYS A 8
SITE 2 AC1 8 ARG A 9 GLU B 1 HIS B 5 LYS B 8
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
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 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000
Complete list - 25 201 Bytes